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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2005-12-30</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001235010</issuerCik>
        <issuerName>MOMENTA PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>MNTA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001294284</rptOwnerCik>
            <rptOwnerName>Venkataraman Ganesh</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O MOMENTA PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>675 WEST KENDALL STREET</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Senior V.P., Research</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.99</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2005-12-30</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>31200</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.99</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-04-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>7200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>95400</value>
                    <footnoteId id="F4"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.91</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2005-12-30</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>31200</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>4.91</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-04-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>31200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>95400</value>
                    <footnoteId id="F4"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">On December 30, 2005, in an effort to avoid adverse tax consequences to the Reporting Person under 409A of the Internal Revenue Code, the Issuer and the Reporting Person amended an oustanding stock option to purchase 38,400 shares with an exercise price of $0.99 per share (the &quot;Original Option&quot;). As amended, the portion of the Original Option vested as of December 31, 2004, or 7,200 shares, shall remain in full force and effect and continue to have an exercise price of $0.99. The remaining portion of the Original Option shall be deemed to be cancelled and a replacement option for the purchase of 31,200 shares shall be deemed granted to the Reporting Person with an increased exercise price equal to $4.91 (the &quot;Replacement Option&quot;).</footnote>
        <footnote id="F2">As of December 31, 2004, the Original Option was vested as to 7,200 shares, and the reporting person may exercise such option as to such number of shares for a per share exercise price of $0.99.</footnote>
        <footnote id="F3">As of January 1, 2006, the Replacement Option was vested as to 12,000 shares, and the Reporting Person may exercise such option as to such number of shares for a per share exercise price of $4.91.  The remaining portion of the Replacement Option vests as to 6.25% of the shares at the end of each three-month period following January 1, 2006.</footnote>
        <footnote id="F4">Includes multiple option grants with different prices and vesting dates.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Ganesh Venkataraman</signatureName>
        <signatureDate>2006-01-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
