<?xml version="1.0" encoding="us-ascii"?>
<!-- DFS ActiveDisclosure(SM) XBRL Linkbase Document - http://www.dfsco.com/financial-services/ -->
<!-- Creation Date      : 2017-12-07T17:06:06.0095163+00:00 -->
<!-- Version            : 2.5.0.9 -->
<!-- Package ID         : 1350BB4E8F1C1D3AF9D718BDCF0FC4E4-0001177648-001706 -->
<!-- Copyright (c) 2017 Donnelley Financial, LLC. All Rights Reserved. -->
<linkbase xmlns="http://www.xbrl.org/2003/linkbase" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xlink="http://www.w3.org/1999/xlink" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <roleRef xlink:type="simple" xlink:href="enta-20170930.xsd#TemplateLink" roleURI="http://www.enanta.com/20170930/role/TemplateLink" />
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/StatementConsolidatedBalanceSheets" xlink:href="enta-20170930.xsd#Role_StatementConsolidatedBalanceSheets" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/StatementConsolidatedBalanceSheets">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:type="locator" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccountsReceivableNetCurrent" xlink:type="locator" xlink:label="us-gaap_AccountsReceivableNetCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesCurrent" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedCashAndCashEquivalentsNoncurrent" xlink:type="locator" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsNoncurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsLiabilitiesNetNoncurrent" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsLiabilitiesNetNoncurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesNoncurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AssetsCurrent" xlink:type="locator" xlink:label="us-gaap_AssetsCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_Assets" xlink:type="locator" xlink:label="us-gaap_Assets" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccruedIncomeTaxesCurrent" xlink:type="locator" xlink:label="us-gaap_AccruedIncomeTaxesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccountsPayableCurrent" xlink:type="locator" xlink:label="us-gaap_AccountsPayableCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OtherLiabilitiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesNoncurrent" />
    <loc xlink:href="enta-20170930.xsd#enta_NonConvertiblePreferredStockLiabilities" xlink:type="locator" xlink:label="enta_NonConvertiblePreferredStockLiabilities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_WarrantsAndRightsOutstanding" xlink:type="locator" xlink:label="us-gaap_WarrantsAndRightsOutstanding" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_LiabilitiesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:type="locator" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" xlink:type="locator" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:type="locator" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockValue" xlink:type="locator" xlink:label="us-gaap_CommonStockValue" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StockholdersEquity" xlink:type="locator" xlink:label="us-gaap_StockholdersEquity" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommitmentsAndContingencies" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingencies" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_Liabilities" xlink:type="locator" xlink:label="us-gaap_Liabilities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:type="locator" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_Liabilities" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_CommitmentsAndContingencies" order="10020.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_StockholdersEquity" order="10030.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_CommonStockValue" order="10040.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_AdditionalPaidInCapitalCommonStock" order="10050.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" order="10060.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="10070.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_LiabilitiesCurrent" order="10080.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_WarrantsAndRightsOutstanding" order="10090.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="enta_NonConvertiblePreferredStockLiabilities" order="10100.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_OtherLiabilitiesNoncurrent" order="10110.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccountsPayableCurrent" order="10120.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="10130.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccruedIncomeTaxesCurrent" order="10140.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_AssetsCurrent" order="10150.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" order="10160.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_AvailableForSaleSecuritiesNoncurrent" order="10170.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_DeferredTaxAssetsLiabilitiesNetNoncurrent" order="10180.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_RestrictedCashAndCashEquivalentsNoncurrent" order="10190.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" order="10200.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_AvailableForSaleSecuritiesCurrent" order="10210.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_AccountsReceivableNetCurrent" order="10220.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" order="10230.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/StatementConsolidatedStatementsOfOperations" xlink:href="enta-20170930.xsd#Role_StatementConsolidatedStatementsOfOperations" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/StatementConsolidatedStatementsOfOperations">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RevenueFromGrants" xlink:type="locator" xlink:label="us-gaap_RevenueFromGrants" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RoyaltyRevenue" xlink:type="locator" xlink:label="us-gaap_RoyaltyRevenue" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RevenueRecognitionMilestoneMethodRevenueRecognized" xlink:type="locator" xlink:label="us-gaap_RevenueRecognitionMilestoneMethodRevenueRecognized" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:type="locator" xlink:label="us-gaap_GeneralAndAdministrativeExpense" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:type="locator" xlink:label="us-gaap_ResearchAndDevelopmentExpense" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CostsAndExpenses" xlink:type="locator" xlink:label="us-gaap_CostsAndExpenses" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_Revenues" xlink:type="locator" xlink:label="us-gaap_Revenues" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DerivativeInstrumentsNotDesignatedAsHedgingInstrumentsGainLossNet" xlink:type="locator" xlink:label="us-gaap_DerivativeInstrumentsNotDesignatedAsHedgingInstrumentsGainLossNet" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_InterestExpense" xlink:type="locator" xlink:label="us-gaap_InterestExpense" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_InvestmentIncomeInterest" xlink:type="locator" xlink:label="us-gaap_InvestmentIncomeInterest" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_NonoperatingIncomeExpense" xlink:type="locator" xlink:label="us-gaap_NonoperatingIncomeExpense" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OperatingIncomeLoss" xlink:type="locator" xlink:label="us-gaap_OperatingIncomeLoss" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncomeTaxExpenseBenefit" xlink:type="locator" xlink:label="us-gaap_IncomeTaxExpenseBenefit" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:type="locator" xlink:label="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_IncomeTaxExpenseBenefit" order="10020.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:to="us-gaap_OperatingIncomeLoss" order="10030.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeLossFromContinuingOperationsBeforeIncomeTaxesExtraordinaryItemsNoncontrollingInterest" xlink:to="us-gaap_NonoperatingIncomeExpense" order="10040.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NonoperatingIncomeExpense" xlink:to="us-gaap_InvestmentIncomeInterest" order="10050.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NonoperatingIncomeExpense" xlink:to="us-gaap_InterestExpense" order="10060.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NonoperatingIncomeExpense" xlink:to="us-gaap_DerivativeInstrumentsNotDesignatedAsHedgingInstrumentsGainLossNet" order="10070.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_Revenues" order="10080.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_CostsAndExpenses" order="10090.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CostsAndExpenses" xlink:to="us-gaap_ResearchAndDevelopmentExpense" order="10100.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CostsAndExpenses" xlink:to="us-gaap_GeneralAndAdministrativeExpense" order="10110.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Revenues" xlink:to="us-gaap_RevenueRecognitionMilestoneMethodRevenueRecognized" order="10120.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Revenues" xlink:to="us-gaap_RoyaltyRevenue" order="10130.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Revenues" xlink:to="us-gaap_RevenueFromGrants" order="10140.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/StatementConsolidatedStatementsOfComprehensiveIncome" xlink:href="enta-20170930.xsd#Role_StatementConsolidatedStatementsOfComprehensiveIncome" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/StatementConsolidatedStatementsOfComprehensiveIncome">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OtherComprehensiveIncomeLossNetOfTax" xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeLossNetOfTax" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ComprehensiveIncomeNetOfTax" xlink:type="locator" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_NetIncomeLoss" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_OtherComprehensiveIncomeLossNetOfTax" order="10020.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherComprehensiveIncomeLossNetOfTax" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" order="10030.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/StatementConsolidatedStatementsOfCashFlows" xlink:href="enta-20170930.xsd#Role_StatementConsolidatedStatementsOfCashFlows" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/StatementConsolidatedStatementsOfCashFlows">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncreaseDecreaseInOtherNoncurrentLiabilities" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOtherNoncurrentLiabilities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncreaseDecreaseInAccruedIncomeTaxesPayable" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccruedIncomeTaxesPayable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncreaseDecreaseInAccruedLiabilities" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccruedLiabilities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsPayable" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncreaseDecreaseInUnbilledReceivables" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInUnbilledReceivables" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccountsReceivable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OtherNoncashIncomeExpense" xlink:type="locator" xlink:label="us-gaap_OtherNoncashIncomeExpense" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DerivativeInstrumentsNotDesignatedAsHedgingInstrumentsGainLossNet" xlink:type="locator" xlink:label="us-gaap_DerivativeInstrumentsNotDesignatedAsHedgingInstrumentsGainLossNet" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ExcessTaxBenefitFromShareBasedCompensationOperatingActivities" xlink:type="locator" xlink:label="us-gaap_ExcessTaxBenefitFromShareBasedCompensationOperatingActivities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" xlink:type="locator" xlink:label="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" />
    <loc xlink:href="enta-20170930.xsd#enta_PremiumOnMarketableSecurities" xlink:type="locator" xlink:label="enta_PremiumOnMarketableSecurities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredIncomeTaxesAndTaxCredits" xlink:type="locator" xlink:label="us-gaap_DeferredIncomeTaxesAndTaxCredits" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DepreciationAndAmortization" xlink:type="locator" xlink:label="us-gaap_DepreciationAndAmortization" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensation" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PaymentsForProceedsFromOtherInvestingActivities" xlink:type="locator" xlink:label="us-gaap_PaymentsForProceedsFromOtherInvestingActivities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ProceedsFromSaleOfAvailableForSaleSecurities" xlink:type="locator" xlink:label="us-gaap_ProceedsFromSaleOfAvailableForSaleSecurities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" xlink:type="locator" xlink:label="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PaymentsToAcquireMarketableSecurities" xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquireMarketableSecurities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RepaymentsOfLongTermCapitalLeaseObligations" xlink:type="locator" xlink:label="us-gaap_RepaymentsOfLongTermCapitalLeaseObligations" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation" xlink:type="locator" xlink:label="us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ExcessTaxBenefitFromShareBasedCompensationFinancingActivities" xlink:type="locator" xlink:label="us-gaap_ExcessTaxBenefitFromShareBasedCompensationFinancingActivities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ProceedsFromStockOptionsExercised" xlink:type="locator" xlink:label="us-gaap_ProceedsFromStockOptionsExercised" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" order="10020.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" order="10030.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:to="us-gaap_ProceedsFromStockOptionsExercised" order="10040.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:to="us-gaap_ExcessTaxBenefitFromShareBasedCompensationFinancingActivities" order="10050.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:to="us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation" order="10060.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:to="us-gaap_RepaymentsOfLongTermCapitalLeaseObligations" order="10070.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" xlink:to="us-gaap_PaymentsToAcquireMarketableSecurities" order="10080.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" xlink:to="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" order="10090.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" xlink:to="us-gaap_ProceedsFromSaleOfAvailableForSaleSecurities" order="10100.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" order="10110.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" xlink:to="us-gaap_PaymentsForProceedsFromOtherInvestingActivities" order="10120.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_NetIncomeLoss" order="10130.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_ShareBasedCompensation" order="10140.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_DepreciationAndAmortization" order="10150.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_DeferredIncomeTaxesAndTaxCredits" order="10160.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="enta_PremiumOnMarketableSecurities" order="10170.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" order="10180.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_ExcessTaxBenefitFromShareBasedCompensationOperatingActivities" order="10190.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_DerivativeInstrumentsNotDesignatedAsHedgingInstrumentsGainLossNet" order="10200.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_OtherNoncashIncomeExpense" order="10210.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInAccountsReceivable" order="10220.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInUnbilledReceivables" order="10230.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" order="10240.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayable" order="10250.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInAccruedLiabilities" order="10260.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInAccruedIncomeTaxesPayable" order="10270.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInOtherNoncurrentLiabilities" order="10280.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosureFairValueOfFinancialAssetsAndLiabilitiesFinancialAssetsAndLiabilitiesThatWereSubjectToFairValueMeasurementOnRecurringBasisDetail" xlink:href="enta-20170930.xsd#Role_DisclosureFairValueOfFinancialAssetsAndLiabilitiesFinancialAssetsAndLiabilitiesThatWereSubjectToFairValueMeasurementOnRecurringBasisDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosureFairValueOfFinancialAssetsAndLiabilitiesFinancialAssetsAndLiabilitiesThatWereSubjectToFairValueMeasurementOnRecurringBasisDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecurities" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecurities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AssetsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_AssetsFairValueDisclosure" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueMeasurementWithUnobservableInputsReconciliationsRecurringBasisLiabilityValue" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementWithUnobservableInputsReconciliationsRecurringBasisLiabilityValue" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_LiabilitiesFairValueDisclosure" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesFairValueDisclosure" xlink:to="us-gaap_FairValueMeasurementWithUnobservableInputsReconciliationsRecurringBasisLiabilityValue" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsFairValueDisclosure" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="10030.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsFairValueDisclosure" xlink:to="us-gaap_AvailableForSaleSecurities" order="10060.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosureMarketableSecuritiesFairValueOfAvailableForSaleMarketableSecuritiesByTypeOfSecurityDetail" xlink:href="enta-20170930.xsd#Role_DisclosureMarketableSecuritiesFairValueOfAvailableForSaleMarketableSecuritiesByTypeOfSecurityDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosureMarketableSecuritiesFairValueOfAvailableForSaleMarketableSecuritiesByTypeOfSecurityDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecurities" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecurities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesAmortizedCost" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:to="us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" order="10010.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:to="us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" order="10020.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:to="us-gaap_AvailableForSaleSecurities" order="10030.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosurePropertyAndEquipmentScheduleOfPropertyAndEquipmentDetail" xlink:href="enta-20170930.xsd#Role_DisclosurePropertyAndEquipmentScheduleOfPropertyAndEquipmentDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosurePropertyAndEquipmentScheduleOfPropertyAndEquipmentDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" xlink:type="locator" xlink:label="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PropertyPlantAndEquipmentGross" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentGross" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertyPlantAndEquipmentNet" xlink:to="us-gaap_PropertyPlantAndEquipmentGross" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_PropertyPlantAndEquipmentNet" xlink:to="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" order="10020.00" priority="2" use="optional" weight="-1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosureAccruedExpensesOtherCurrentLiabilitiesAndOtherLongTermLiabilitiesAccruedExpensesOtherCurrentLiabilitiesAndOtherLongTermLiabilitiesDetail" xlink:href="enta-20170930.xsd#Role_DisclosureAccruedExpensesOtherCurrentLiabilitiesAndOtherLongTermLiabilitiesAccruedExpensesOtherCurrentLiabilitiesAndOtherLongTermLiabilitiesDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosureAccruedExpensesOtherCurrentLiabilitiesAndOtherLongTermLiabilitiesAccruedExpensesOtherCurrentLiabilitiesAndOtherLongTermLiabilitiesDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OtherAccruedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_OtherAccruedLiabilitiesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeaseObligationsCurrent" xlink:type="locator" xlink:label="us-gaap_CapitalLeaseObligationsCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccruedProfessionalFeesCurrent" xlink:type="locator" xlink:label="us-gaap_AccruedProfessionalFeesCurrent" />
    <loc xlink:href="enta-20170930.xsd#enta_AccruedLiabilitiesManufacturing" xlink:type="locator" xlink:label="enta_AccruedLiabilitiesManufacturing" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_EmployeeRelatedLiabilitiesCurrent" />
    <loc xlink:href="enta-20170930.xsd#enta_AccruedPreclinicalAndClinicalExpensesCurrent" xlink:type="locator" xlink:label="enta_AccruedPreclinicalAndClinicalExpensesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AssetRetirementObligationsNoncurrent" xlink:type="locator" xlink:label="us-gaap_AssetRetirementObligationsNoncurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeaseObligationsNoncurrent" xlink:type="locator" xlink:label="us-gaap_CapitalLeaseObligationsNoncurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccruedRentNoncurrent" xlink:type="locator" xlink:label="us-gaap_AccruedRentNoncurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilityForUncertainTaxPositionsNoncurrent" xlink:type="locator" xlink:label="us-gaap_LiabilityForUncertainTaxPositionsNoncurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OtherLiabilitiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesNoncurrent" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherLiabilitiesNoncurrent" xlink:to="us-gaap_LiabilityForUncertainTaxPositionsNoncurrent" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherLiabilitiesNoncurrent" xlink:to="us-gaap_AccruedRentNoncurrent" order="10020.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherLiabilitiesNoncurrent" xlink:to="us-gaap_CapitalLeaseObligationsNoncurrent" order="10030.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OtherLiabilitiesNoncurrent" xlink:to="us-gaap_AssetRetirementObligationsNoncurrent" order="10040.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="enta_AccruedPreclinicalAndClinicalExpensesCurrent" order="10050.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_EmployeeRelatedLiabilitiesCurrent" order="10060.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="enta_AccruedLiabilitiesManufacturing" order="10070.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_AccruedProfessionalFeesCurrent" order="10080.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_CapitalLeaseObligationsCurrent" order="10090.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AccruedLiabilitiesCurrent" xlink:to="us-gaap_OtherAccruedLiabilitiesCurrent" order="10100.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosureNetIncomePerShareBasicAndDilutedNetIncomePerCommonShareDetail" xlink:href="enta-20170930.xsd#Role_DisclosureNetIncomePerShareBasicAndDilutedNetIncomePerCommonShareDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosureNetIncomePerShareBasicAndDilutedNetIncomePerCommonShareDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustment" xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustment" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:to="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:to="us-gaap_WeightedAverageNumberDilutedSharesOutstandingAdjustment" order="10020.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosureCommitmentsAndContingenciesFutureMinimumLeasePaymentsDetail" xlink:href="enta-20170930.xsd#Role_DisclosureCommitmentsAndContingenciesFutureMinimumLeasePaymentsDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosureCommitmentsAndContingenciesFutureMinimumLeasePaymentsDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueThereafter" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueThereafter" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFiveYears" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFiveYears" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFourYears" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFourYears" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueInThreeYears" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInThreeYears" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueInTwoYears" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInTwoYears" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueCurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDue" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueThereafter" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueThereafter" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFiveYears" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFiveYears" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFourYears" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFourYears" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueInThreeYears" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInThreeYears" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueInTwoYears" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInTwoYears" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueCurrent" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDue" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueCurrent" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInTwoYears" order="10020.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInThreeYears" order="10030.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFourYears" order="10040.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFiveYears" order="10050.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueThereafter" order="10060.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueCurrent" order="10070.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInTwoYears" order="10080.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInThreeYears" order="10090.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFourYears" order="10100.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFiveYears" order="10110.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueThereafter" order="10120.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosureIncomeTaxesSummaryOfIncomeTaxExpenseDetail" xlink:href="enta-20170930.xsd#Role_DisclosureIncomeTaxesSummaryOfIncomeTaxExpenseDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosureIncomeTaxesSummaryOfIncomeTaxExpenseDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredStateAndLocalIncomeTaxExpenseBenefit" xlink:type="locator" xlink:label="us-gaap_DeferredStateAndLocalIncomeTaxExpenseBenefit" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredFederalIncomeTaxExpenseBenefit" xlink:type="locator" xlink:label="us-gaap_DeferredFederalIncomeTaxExpenseBenefit" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CurrentStateAndLocalTaxExpenseBenefit" xlink:type="locator" xlink:label="us-gaap_CurrentStateAndLocalTaxExpenseBenefit" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CurrentFederalTaxExpenseBenefit" xlink:type="locator" xlink:label="us-gaap_CurrentFederalTaxExpenseBenefit" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncomeTaxExpenseBenefit" xlink:type="locator" xlink:label="us-gaap_IncomeTaxExpenseBenefit" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeTaxExpenseBenefit" xlink:to="us-gaap_CurrentFederalTaxExpenseBenefit" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeTaxExpenseBenefit" xlink:to="us-gaap_CurrentStateAndLocalTaxExpenseBenefit" order="10020.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeTaxExpenseBenefit" xlink:to="us-gaap_DeferredFederalIncomeTaxExpenseBenefit" order="10030.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_IncomeTaxExpenseBenefit" xlink:to="us-gaap_DeferredStateAndLocalIncomeTaxExpenseBenefit" order="10040.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosureIncomeTaxesReconciliationOfIncomeTaxProvisionAtFederalStatutoryIncomeTaxRateAndEffectiveTaxRateDetail" xlink:href="enta-20170930.xsd#Role_DisclosureIncomeTaxesReconciliationOfIncomeTaxProvisionAtFederalStatutoryIncomeTaxRateAndEffectiveTaxRateDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosureIncomeTaxesReconciliationOfIncomeTaxProvisionAtFederalStatutoryIncomeTaxRateAndEffectiveTaxRateDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationOtherAdjustments" xlink:type="locator" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationOtherAdjustments" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationChangeInEnactedTaxRate" xlink:type="locator" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationChangeInEnactedTaxRate" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationNondeductibleExpenseShareBasedCompensationCost" xlink:type="locator" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationNondeductibleExpenseShareBasedCompensationCost" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationTaxCreditsResearch" xlink:type="locator" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationTaxCreditsResearch" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationStateAndLocalIncomeTaxes" xlink:type="locator" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationStateAndLocalIncomeTaxes" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EffectiveIncomeTaxRateReconciliationAtFederalStatutoryIncomeTaxRate" xlink:type="locator" xlink:label="us-gaap_EffectiveIncomeTaxRateReconciliationAtFederalStatutoryIncomeTaxRate" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:type="locator" xlink:label="us-gaap_EffectiveIncomeTaxRateContinuingOperations" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationAtFederalStatutoryIncomeTaxRate" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationStateAndLocalIncomeTaxes" order="10020.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationTaxCreditsResearch" order="10030.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationNondeductibleExpenseShareBasedCompensationCost" order="10040.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationChangeInEnactedTaxRate" order="10050.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_EffectiveIncomeTaxRateContinuingOperations" xlink:to="us-gaap_EffectiveIncomeTaxRateReconciliationOtherAdjustments" order="10060.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
  <roleRef roleURI="http://www.enanta.com/20170930/taxonomy/role/DisclosureIncomeTaxesNetDeferredTaxAssetsAndLiabilitiesDetail" xlink:href="enta-20170930.xsd#Role_DisclosureIncomeTaxesNetDeferredTaxAssetsAndLiabilitiesDetail" xlink:type="simple" />
  <calculationLink xlink:type="extended" xlink:role="http://www.enanta.com/20170930/taxonomy/role/DisclosureIncomeTaxesNetDeferredTaxAssetsAndLiabilitiesDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsOtherComprehensiveLoss" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsOtherComprehensiveLoss" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsOther" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsOther" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsInProcessResearchAndDevelopment" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsInProcessResearchAndDevelopment" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsTaxDeferredExpenseCompensationAndBenefitsShareBasedCompensationCost" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsTaxDeferredExpenseCompensationAndBenefitsShareBasedCompensationCost" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsValuationAllowance" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsValuationAllowance" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsGross" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsGross" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxLiabilitiesOtherComprehensiveIncome" xlink:type="locator" xlink:label="us-gaap_DeferredTaxLiabilitiesOtherComprehensiveIncome" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxLiabilitiesPrepaidExpenses" xlink:type="locator" xlink:label="us-gaap_DeferredTaxLiabilitiesPrepaidExpenses" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxLiabilitiesPropertyPlantAndEquipment" xlink:type="locator" xlink:label="us-gaap_DeferredTaxLiabilitiesPropertyPlantAndEquipment" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredIncomeTaxLiabilities" xlink:type="locator" xlink:label="us-gaap_DeferredIncomeTaxLiabilities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsNet" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsNet" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredTaxAssetsLiabilitiesNet" xlink:type="locator" xlink:label="us-gaap_DeferredTaxAssetsLiabilitiesNet" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsLiabilitiesNet" xlink:to="us-gaap_DeferredTaxAssetsNet" order="10010.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsLiabilitiesNet" xlink:to="us-gaap_DeferredIncomeTaxLiabilities" order="10020.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredIncomeTaxLiabilities" xlink:to="us-gaap_DeferredTaxLiabilitiesPropertyPlantAndEquipment" order="10030.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredIncomeTaxLiabilities" xlink:to="us-gaap_DeferredTaxLiabilitiesPrepaidExpenses" order="10040.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredIncomeTaxLiabilities" xlink:to="us-gaap_DeferredTaxLiabilitiesOtherComprehensiveIncome" order="10050.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsNet" xlink:to="us-gaap_DeferredTaxAssetsGross" order="10060.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsNet" xlink:to="us-gaap_DeferredTaxAssetsValuationAllowance" order="10070.00" priority="2" use="optional" weight="-1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsTaxDeferredExpenseCompensationAndBenefitsShareBasedCompensationCost" order="10080.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsInProcessResearchAndDevelopment" order="10090.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsOther" order="10100.00" priority="2" use="optional" weight="1.00" />
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_DeferredTaxAssetsGross" xlink:to="us-gaap_DeferredTaxAssetsOtherComprehensiveLoss" order="10110.00" priority="2" use="optional" weight="1.00" />
  </calculationLink>
</linkbase>
