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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2013-10-24</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001142576</issuerCik>
        <issuerName>OPTIMER PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>OPTR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001570990</rptOwnerCik>
            <rptOwnerName>Schaum Meredith</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>101 HUDSON STREET</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3501</rptOwnerStreet2>
            <rptOwnerCity>JERSEY CITY</rptOwnerCity>
            <rptOwnerState>NJ</rptOwnerState>
            <rptOwnerZipCode>07302</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Gen Counsel and Chief Comp Off</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common stock</value>
            </securityTitle>
            <transactionDate>
                <value>2013-10-24</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2937</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>10.75</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.72</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2013-10-24</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>30000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.06</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2023-02-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>30000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Includes 1,148 shares acquired under the Optimer Pharmaceuticals, Inc. (&quot;Optimer&quot;) employee stock purchase plan on October 22, 2013.</footnote>
        <footnote id="F2">Pursuant to the Agreement and Plan of Merger, dated as of July 30, 2013 (the &quot;Merger Agreement&quot;), among Optimer, Cubist Pharmaceuticals, Inc. (&quot;Cubist&quot;), and PDRS Corporation, shares were converted into the right to receive per share consideration of: (i) $10.75 cash and (ii) one contingent value right issued by Cubist in accordance with the Contingent Value Rights Agreement, dated as of October 24, 2013, between Cubist and American Stock Transfer &amp; Trust Company, LLC (together, the &quot;Per Share Merger Consideration&quot;).</footnote>
        <footnote id="F3">Pursuant to the terms of the Merger Agreement, each option was fully vested and converted into the right to receive a cash payment equal to the excess, if any, of $12.78 (the last reported sale price of a share of Optimer common stock on The NASDAQ Global Select Market on October 23, 2013) over such option's per share exercise price.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Meredith Schaum</signatureName>
        <signatureDate>2013-10-28</signatureDate>
    </ownerSignature>
</ownershipDocument>
