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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2014-04-17</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001345709</rptOwnerCik>
            <rptOwnerName>Nash Sarah E</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>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2014-04-17</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>5</transactionFormType>
                <transactionCode>G</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value>E</value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>36698</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>940296</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Trust</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2014-05-07</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>15000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>6.79</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>955296</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">The reporting person was previously a trustee of a grantor retained annuity trust. All shares of the issuer held by such trust were previously reported as beneficially owned by the reporting person on a Form 3 filed on 2/1/12. The reported transaction represents the termination of such trust and the distribution of a portion of the shares held by such trust to beneficiaries not reportable by the reporting person. The remaining 27,750 shares held by such trust were distributed to the reporting person and continue to be reported in this Form 4 as directly owned.</footnote>
        <footnote id="F2">The price reported in Column 4 is a weighted average price. These shares were purchased in multiple transactions at prices ranging from $6.74 to $6.81, inclusive. The reporting person undertakes to provide to the Issuer, any security holder of the Issuer or the Staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares purchased at each separate price within such range.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Jeffrey A. Munsie, attorney-in-fact</signatureName>
        <signatureDate>2014-05-09</signatureDate>
    </ownerSignature>
</ownershipDocument>
