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

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2006-08-18</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000356830</issuerCik>
        <issuerName>OSCIENT PHARMACEUTICALS CORP</issuerName>
        <issuerTradingSymbol>OSCI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001218156</rptOwnerCik>
            <rptOwnerName>PAUL ROYALTY FUND II L P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O PAUL CAPITAL PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>50 CALIFORNIA STREET, SUITE 3000</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001373654</rptOwnerCik>
            <rptOwnerName>Paul Royalty Fund Holdings II</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O PAUL CAPITAL PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>50 CALIFORNIA STREET, SUITE 3000</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001373653</rptOwnerCik>
            <rptOwnerName>Paul Royalty Associates II, LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O PAUL CAPITAL PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>50 CALIFORNIA STREET, SUITE 3000</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001373652</rptOwnerCik>
            <rptOwnerName>Paul Royalty Management, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O PAUL CAPITAL PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>50 CALIFORNIA STREET, SUITE 3000</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001373656</rptOwnerCik>
            <rptOwnerName>Paul Capital Advisors, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O PAUL CAPITAL PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>50 CALIFORNIA STREET, SUITE 3000</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, $0.10 par value</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>11111111</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Common Stock Warrants</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.86</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2006-08-18</value>
            </exerciseDate>
            <expirationDate>
                <value>2013-08-17</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2304147</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Foonotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">This report is filed jointly by Paul Royalty Fund Holdings II (&quot;PRFH&quot;), Paul Royalty Fund II, LP (&quot;PRF&quot;), Paul Royalty Associates II, LP (&quot;PRA&quot;), Paul Royalty Management, LLC (&quot;PRM&quot;), Paul Capital Advisors, LLC (&quot;PCA&quot;).  PRFH directly owns 11,111,111 shares of Common Stock.  &quot;).  PRF and PRA may be deemed to indirectly own 11,111,111 shares of common stock held by PRFH because PRF and PRA are the general partners of PRFH.  PRM may be deemed to indirectly own the shares because PRM is the general partner of PRF and PRA.  As manager of PRA, PCA exercises voting and dispositive power over investments held by PRA.</footnote>
        <footnote id="F2">PRFH is the record owner of warrants, exercisable for 2,304,147  shares of Common Stock.  PRF and PRA may be deemed to own the warrants, exercisable for 2,304,147 shares of Common Stock, held by PRFH because PRF and PRA are the general partners of PRFH.  PRM may be deemed to own the warrants because PRM is the general partner of PRF and PRA.  As manager of PRA, PCA exercises voting and dispositive power over investments held by PRA.</footnote>
    </footnotes>

    <remarks>Gregory B. Brown, MD is a member of PCA, and he serves on the Board of Managers of PCA.  Additionally, Dr. Brown has been elected to the Board of Directors of Oscient Pharmaceuticals Corporation pursuant to that certain Common Stock Purchase and Warrant Agreement, dated July 21, 2006, by and between Oscient Pharmaceuticals Corporation and PRFH.  Dr. Brown files his own Section 16 reports.</remarks>

    <ownerSignature>
        <signatureName>PAUL ROYALTY FUND HOLDINGS II By: Paul Royalty Fund II, LP, its Managing Partner By: Paul Royalty Management, LLC, its General Partner By: Paul Capital Advisors, LLC, its Manager, By: /s/ Gregory B. Brown, MD</signatureName>
        <signatureDate>2006-08-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>PAUL ROYALTY FUND II, LP, By: Paul Royalty Management, LLC, its General Partner By: Paul Capital Advisors, LLC, its Manager, By: /s/ Gregory B. Brown, MD</signatureName>
        <signatureDate>2006-08-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>PAUL ROYALTY ASSOCIATES, LP By: Paul Royalty Management, LLC, its General Partner, By: Paul Capital Advisors, By: /s/ Gregory B. Brown, MD</signatureName>
        <signatureDate>2006-08-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>PAUL CAPITAL ROYALTY MANAGEMENT, LLC, By: Paul Capital Advisors, LLC, its Manager, By: /s/ Gregory B. Brown, MD</signatureName>
        <signatureDate>2006-08-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>PAUL CAPITAL ADVISORS, LLC, By: /s/ Gregory B. Brown, MD</signatureName>
        <signatureDate>2006-08-28</signatureDate>
    </ownerSignature>
</ownershipDocument>
