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

    <schemaVersion>X0205</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2012-06-13</periodOfReport>

    <noSecuritiesOwned>1</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001274792</issuerCik>
        <issuerName>MERRIMACK PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>MACK</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001234382</rptOwnerCik>
            <rptOwnerName>MENDELSOHN JOHN</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O MERRIMACK PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>ONE KENDALL SQUARE, SUITE B7201</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02139</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes></footnotes>

    <ownerSignature>
        <signatureName>/s/ Jeffrey A. Munsie, attorney-in-fact</signatureName>
        <signatureDate>2012-06-19</signatureDate>
    </ownerSignature>
</ownershipDocument>
