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<!-- DFIN ActiveDisclosure(SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2019-11-27T00:54:55.4857642+00:00 -->
<!-- Version            : 5.0.1.294 -->
<!-- Package ID         : 24ae80a6d3284a4d8f852abf6441e51a -->
<!-- Copyright (c) 2019 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
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  <xsd:element id="enta_ScenarioThreeMember" name="ScenarioThreeMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_ScenarioFourMember" name="ScenarioFourMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_ScenarioFiveMember" name="ScenarioFiveMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_PeriodFromFirstCommercialSaleOfCoveredProductForContinuationOfRightsAndObligationsUnderAgreement" name="PeriodFromFirstCommercialSaleOfCoveredProductForContinuationOfRightsAndObligationsUnderAgreement" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_PreferredStockMaximumRedemptionPeriod" name="PreferredStockMaximumRedemptionPeriod" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRightsExpirationDate" name="ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRightsExpirationDate" type="xbrli:dateItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_TwoThousandNineteenEquityIncentivePlanMember" name="TwoThousandNineteenEquityIncentivePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_EmployeeStockPurchasePlanMember" name="EmployeeStockPurchasePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_EmployeesMember" name="EmployeesMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_PerformanceBasedOptionsMember" name="PerformanceBasedOptionsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_CertainExecutivesMember" name="CertainExecutivesMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_ShareBasedPaymentAwardStockOptionsValuationAssumptionsLineItems" name="ShareBasedPaymentAwardStockOptionsValuationAssumptionsLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_ShareBasedPaymentAwardStockOptionsValuationAssumptionsTable" name="ShareBasedPaymentAwardStockOptionsValuationAssumptionsTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAggregateIntrinsicValueAbstract" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAggregateIntrinsicValueAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsAggregateGrantDateFairValue" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsAggregateGrantDateFairValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="enta_ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfTargetSharesEarnedMinimumLimit" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfTargetSharesEarnedMinimumLimit" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfTargetSharesEarnedMaximumLimit" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfTargetSharesEarnedMaximumLimit" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_ShareBasedCompensationArrangementRTSRUAwardFairValueAssumptionsRiskFreeInterestRate" name="ShareBasedCompensationArrangementRTSRUAwardFairValueAssumptionsRiskFreeInterestRate" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_ShareBasedCompensationArrangementRTSRUAwardFairValueAssumptionsExpectedDividendRate" name="ShareBasedCompensationArrangementRTSRUAwardFairValueAssumptionsExpectedDividendRate" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfTargetSharesVested" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfTargetSharesVested" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_ShareBasedCompensationArrangementByShareBasedPaymentAwardAggregateOfTargetShareIssued" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardAggregateOfTargetShareIssued" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_NumberOfLeases" name="NumberOfLeases" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_CommitmentsAndContingenciesLineItems" name="CommitmentsAndContingenciesLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_CommitmentsAndContingenciesTable" name="CommitmentsAndContingenciesTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_FirstLeaseMember" name="FirstLeaseMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_FiveHundredArsenalStreetWatertownMassachusettsMember" name="FiveHundredArsenalStreetWatertownMassachusettsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_SecondLeaseMember" name="SecondLeaseMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_FourHundredTalcottAvenueWatertownMassachusettsMember" name="FourHundredTalcottAvenueWatertownMassachusettsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_EffectivePeriodOfLeaseAgreement" name="EffectivePeriodOfLeaseAgreement" type="xbrli:gYearMonthItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_LeaseExpirationPeriod" name="LeaseExpirationPeriod" type="xbrli:gYearMonthItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_LicenseExpense" name="LicenseExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="enta_EffectiveIncomeTaxRateReconciliationTaxCutAndJobsActOf2017Percent" name="EffectiveIncomeTaxRateReconciliationTaxCutAndJobsActOf2017Percent" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_EffectiveIncomeTaxRateReconciliationForeignDerivedIntangibleIncomePercent" name="EffectiveIncomeTaxRateReconciliationForeignDerivedIntangibleIncomePercent" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_DeferredTaxAssetsCapitalizedResearchAndDevelopmentExpenses" name="DeferredTaxAssetsCapitalizedResearchAndDevelopmentExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="enta_ResearchAndDevelopmentTaxCreditCarryForwardExpirationYear" name="ResearchAndDevelopmentTaxCreditCarryForwardExpirationYear" type="xbrli:gYearItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="enta_ScheduleOfQuarterlyFinancialInformationLineItems" name="ScheduleOfQuarterlyFinancialInformationLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="enta_ScheduleOfQuarterlyFinancialInformationTable" name="ScheduleOfQuarterlyFinancialInformationTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
</xsd:schema>
