<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2006-09-01</periodOfReport>

    <dateOfOriginalSubmission>2006-09-05</dateOfOriginalSubmission>

    <noSecuritiesOwned>1</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000912183</issuerCik>
        <issuerName>CUBIST PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>CBST</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001374065</rptOwnerCik>
            <rptOwnerName>Archer Gordon Lee</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>65 HAYDEN AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>LEXINGTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02421</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <footnotes></footnotes>

    <ownerSignature>
        <signatureName>Christopher D.T. Guiffre, Esq. - Attorney in fact</signatureName>
        <signatureDate>2006-09-05</signatureDate>
    </ownerSignature>
</ownershipDocument>
