<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>5</documentType><periodOfReport>2003-12-31</periodOfReport>
    <form3HoldingsReported>1</form3HoldingsReported>

    <form4TransactionsReported>0</form4TransactionsReported>

    <issuer>
        <issuerCik>0000815838</issuerCik>
        <issuerName>NOVEN PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>NOVN</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001224098</rptOwnerCik>
            <rptOwnerName>MANTELLE JUAN A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O NOVEN PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>11960 S.W. 144TH STREET</rptOwnerStreet2>
            <rptOwnerCity>MIAMI</rptOwnerCity>
            <rptOwnerState>FL</rptOwnerState>
            <rptOwnerZipCode>33186</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>0</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>VP &amp; Chief Technical Officer</officerTitle></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeHolding><securityTitle><value>Common Stock($.0001 Par Value)</value></securityTitle><transactionCoding><transactionFormType>3</transactionFormType><footnoteId id="F1"/></transactionCoding><postTransactionAmounts><sharesOwnedFollowingTransaction><value>18767</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeHolding></nonDerivativeTable><footnotes><footnote id="F1">The reporting person owned a total of 98,039 shares of common stock on June 6, 2000, the date on which the reporting person became an officer of Noven Pharmaceuticals, Inc. and presently owns 18,767 shares of common stock.</footnote></footnotes><remarks/><ownerSignature><signatureName>Juan A. Mantelle</signatureName><signatureDate>2004-01-16</signatureDate></ownerSignature></ownershipDocument>

