<?xml version="1.0" encoding="us-ascii"?>
<!-- DFIN ActiveDisclosure(SM) XBRL Linkbase Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2022-11-10T01:22:22.3290748+00:00 -->
<!-- Version            : 5.0.1.753 -->
<!-- Package ID         : bb3fb43789734269a8a890696d8d7ac9 -->
<!-- Copyright (c) 2022 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef xlink:type="simple" xlink:href="mnov-20220930.xsd#TemplateLink" roleURI="http://www.medicinova.com/20220930/role/TemplateLink" />
  <link:roleRef roleURI="http://www.medicinova.com/20220930/taxonomy/role/StatementCondensedConsolidatedBalanceSheets" xlink:href="mnov-20220930.xsd#Role_StatementCondensedConsolidatedBalanceSheets" xlink:type="simple" />
  <link:calculationLink xlink:type="extended" xlink:role="http://www.medicinova.com/20220930/taxonomy/role/StatementCondensedConsolidatedBalanceSheets">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:type="locator" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherAssetsNoncurrent" xlink:type="locator" xlink:label="us-gaap_OtherAssetsNoncurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" />
    <link:loc xlink:href="mnov-20220930.xsd#mnov_InProcessResearchAndDevelopment" xlink:type="locator" xlink:label="mnov_InProcessResearchAndDevelopment" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_Goodwill" xlink:type="locator" xlink:label="us-gaap_Goodwill" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LongTermInvestments" xlink:type="locator" xlink:label="us-gaap_LongTermInvestments" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AssetsCurrent" xlink:type="locator" xlink:label="us-gaap_AssetsCurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_Assets" xlink:type="locator" xlink:label="us-gaap_Assets" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent" />
    <link:loc xlink:href="mnov-20220930.xsd#mnov_AccruedLiabilitiesAndOtherLiabilitiesCurrent" xlink:type="locator" xlink:label="mnov_AccruedLiabilitiesAndOtherLiabilitiesCurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountsPayableCurrent" xlink:type="locator" xlink:label="us-gaap_AccountsPayableCurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherLiabilitiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_OtherLiabilitiesNoncurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DeferredIncomeTaxLiabilitiesNet" xlink:type="locator" xlink:label="us-gaap_DeferredIncomeTaxLiabilitiesNet" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_LiabilitiesCurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:type="locator" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" xlink:type="locator" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:type="locator" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockValue" xlink:type="locator" xlink:label="us-gaap_CommonStockValue" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockholdersEquity" xlink:type="locator" xlink:label="us-gaap_StockholdersEquity" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommitmentsAndContingencies" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingencies" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_Liabilities" xlink:type="locator" xlink:label="us-gaap_Liabilities" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:type="locator" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity" />
    <link: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" />
    <link: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" />
    <link: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" />
    <link: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" />
    <link: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" />
    <link: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" />
    <link: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" />
    <link: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" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_DeferredIncomeTaxLiabilitiesNet" order="10090.00" priority="2" use="optional" weight="1.00" />
    <link: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="10100.00" priority="2" use="optional" weight="1.00" />
    <link: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="10110.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="mnov_AccruedLiabilitiesAndOtherLiabilitiesCurrent" order="10120.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent" order="10130.00" priority="2" use="optional" weight="1.00" />
    <link: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="10140.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_LongTermInvestments" order="10150.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_Goodwill" order="10160.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="mnov_InProcessResearchAndDevelopment" order="10170.00" priority="2" use="optional" weight="1.00" />
    <link: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="10180.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" order="10190.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_OtherAssetsNoncurrent" order="10200.00" priority="2" use="optional" weight="1.00" />
    <link: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="10210.00" priority="2" use="optional" weight="1.00" />
    <link: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="10220.00" priority="2" use="optional" weight="1.00" />
  </link:calculationLink>
  <link:roleRef roleURI="http://www.medicinova.com/20220930/taxonomy/role/StatementCondensedConsolidatedStatementsOfOperationsAndComprehensiveLoss" xlink:href="mnov-20220930.xsd#Role_StatementCondensedConsolidatedStatementsOfOperationsAndComprehensiveLoss" xlink:type="simple" />
  <link:calculationLink xlink:type="extended" xlink:role="http://www.medicinova.com/20220930/taxonomy/role/StatementCondensedConsolidatedStatementsOfOperationsAndComprehensiveLoss">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:type="locator" xlink:label="us-gaap_GeneralAndAdministrativeExpense" />
    <link:loc xlink:href="mnov-20220930.xsd#mnov_ResearchDevelopmentAndPatentsExpense" xlink:type="locator" xlink:label="mnov_ResearchDevelopmentAndPatentsExpense" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingExpenses" xlink:type="locator" xlink:label="us-gaap_OperatingExpenses" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:type="locator" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherNonoperatingIncomeExpense" xlink:type="locator" xlink:label="us-gaap_OtherNonoperatingIncomeExpense" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InterestIncomeOther" xlink:type="locator" xlink:label="us-gaap_InterestIncomeOther" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingIncomeLoss" xlink:type="locator" xlink:label="us-gaap_OperatingIncomeLoss" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax" xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ComprehensiveIncomeNetOfTax" xlink:type="locator" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax" />
    <link: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" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax" order="10020.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OperatingIncomeLoss" order="10030.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_InterestIncomeOther" order="10040.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OtherNonoperatingIncomeExpense" order="10050.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" order="10060.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_OperatingExpenses" order="10070.00" priority="2" use="optional" weight="-1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses" xlink:to="mnov_ResearchDevelopmentAndPatentsExpense" order="10080.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses" xlink:to="us-gaap_GeneralAndAdministrativeExpense" order="10090.00" priority="2" use="optional" weight="1.00" />
  </link:calculationLink>
  <link:roleRef roleURI="http://www.medicinova.com/20220930/taxonomy/role/StatementCondensedConsolidatedStatementsOfCashFlows" xlink:href="mnov-20220930.xsd#Role_StatementCondensedConsolidatedStatementsOfCashFlows" xlink:type="simple" />
  <link:calculationLink xlink:type="extended" xlink:role="http://www.medicinova.com/20220930/taxonomy/role/StatementCondensedConsolidatedStatementsOfCashFlows">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInOperatingLeaseLiability" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOperatingLeaseLiability" />
    <link:loc xlink:href="mnov-20220930.xsd#mnov_IncreaseDecreaseInAccountsPayableAccruedExpensesAndOtherCurrentLiabilities" xlink:type="locator" xlink:label="mnov_IncreaseDecreaseInAccountsPayableAccruedExpensesAndOtherCurrentLiabilities" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" />
    <link:loc xlink:href="mnov-20220930.xsd#mnov_ChangeInCarryingAmountOfRightOfUseAsset" xlink:type="locator" xlink:label="mnov_ChangeInCarryingAmountOfRightOfUseAsset" />
    <link:loc xlink:href="mnov-20220930.xsd#mnov_NonCashInterestOnInvestments" xlink:type="locator" xlink:label="mnov_NonCashInterestOnInvestments" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DepreciationDepletionAndAmortization" xlink:type="locator" xlink:label="us-gaap_DepreciationDepletionAndAmortization" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensation" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensation" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProfitLoss" xlink:type="locator" xlink:label="us-gaap_ProfitLoss" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsForProceedsFromInvestments" xlink:type="locator" xlink:label="us-gaap_PaymentsForProceedsFromInvestments" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromStockPlans" xlink:type="locator" xlink:label="us-gaap_ProceedsFromStockPlans" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsOfStockIssuanceCosts" xlink:type="locator" xlink:label="us-gaap_PaymentsOfStockIssuanceCosts" />
    <link:loc xlink:href="mnov-20220930.xsd#mnov_ProceedsFromIssuanceOfCommonStockExerciseOfCommonStockOptions" xlink:type="locator" xlink:label="mnov_ProceedsFromIssuanceOfCommonStockExerciseOfCommonStockOptions" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" xlink:type="locator" xlink:label="us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities" order="10010.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities" order="10020.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities" order="10030.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:to="us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" order="10040.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="mnov_ProceedsFromIssuanceOfCommonStockExerciseOfCommonStockOptions" order="10050.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_PaymentsOfStockIssuanceCosts" order="10060.00" priority="2" use="optional" weight="-1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:to="us-gaap_ProceedsFromStockPlans" order="10070.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_PaymentsForProceedsFromInvestments" order="10080.00" priority="2" use="optional" weight="-1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" order="10090.00" priority="2" use="optional" weight="-1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_ProfitLoss" order="10100.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_ShareBasedCompensation" order="10110.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_DepreciationDepletionAndAmortization" order="10120.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="mnov_NonCashInterestOnInvestments" order="10130.00" priority="2" use="optional" weight="-1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="mnov_ChangeInCarryingAmountOfRightOfUseAsset" order="10140.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" order="10150.00" priority="2" use="optional" weight="-1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="mnov_IncreaseDecreaseInAccountsPayableAccruedExpensesAndOtherCurrentLiabilities" order="10160.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:to="us-gaap_IncreaseDecreaseInOperatingLeaseLiability" order="10170.00" priority="2" use="optional" weight="1.00" />
  </link:calculationLink>
  <link:roleRef roleURI="http://www.medicinova.com/20220930/taxonomy/role/DisclosureCommitmentsAndContingenciesScheduleOfRightOfUseAssetsAndRelatedLeaseLiabilitiesDetail" xlink:href="mnov-20220930.xsd#Role_DisclosureCommitmentsAndContingenciesScheduleOfRightOfUseAssetsAndRelatedLeaseLiabilitiesDetail" xlink:type="simple" />
  <link:calculationLink xlink:type="extended" xlink:role="http://www.medicinova.com/20220930/taxonomy/role/DisclosureCommitmentsAndContingenciesScheduleOfRightOfUseAssetsAndRelatedLeaseLiabilitiesDetail">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseLiability" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiability" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeaseLiability" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent" order="10170.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeaseLiability" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent" order="10180.00" priority="2" use="optional" weight="1.00" />
  </link:calculationLink>
  <link:roleRef roleURI="http://www.medicinova.com/20220930/taxonomy/role/DisclosureCommitmentsAndContingenciesScheduleOfMaturitiesOfOperatingLeaseLiabilitiesDetail" xlink:href="mnov-20220930.xsd#Role_DisclosureCommitmentsAndContingenciesScheduleOfMaturitiesOfOperatingLeaseLiabilitiesDetail" xlink:type="simple" />
  <link:calculationLink xlink:type="extended" xlink:role="http://www.medicinova.com/20220930/taxonomy/role/DisclosureCommitmentsAndContingenciesScheduleOfMaturitiesOfOperatingLeaseLiabilitiesDetail">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFive" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFive" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" order="10010.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" order="10020.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" order="10030.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" order="10040.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFive" order="10050.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive" order="10060.00" priority="2" use="optional" weight="1.00" />
  </link:calculationLink>
  <link:roleRef roleURI="http://www.medicinova.com/20220930/taxonomy/role/DisclosureCommitmentsAndContingenciesScheduleOfMaturitiesOfOperatingLeaseLiabilitiesDetail2" xlink:href="mnov-20220930.xsd#Role_DisclosureCommitmentsAndContingenciesScheduleOfMaturitiesOfOperatingLeaseLiabilitiesDetail2" xlink:type="simple" />
  <link:calculationLink xlink:type="extended" xlink:role="http://www.medicinova.com/20220930/taxonomy/role/DisclosureCommitmentsAndContingenciesScheduleOfMaturitiesOfOperatingLeaseLiabilitiesDetail2">
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseLiability" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiability" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" />
    <link:loc xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" order="10010.00" priority="2" use="optional" weight="1.00" />
    <link:calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_OperatingLeaseLiability" order="10020.00" priority="2" use="optional" weight="1.00" />
  </link:calculationLink>
</link:linkbase>
