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

    <schemaVersion>X0304</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2011-11-04</periodOfReport>

    <dateOfOriginalSubmission>2011-11-07</dateOfOriginalSubmission>

    <issuer>
        <issuerCik>0000203527</issuerCik>
        <issuerName>VARIAN MEDICAL SYSTEMS INC</issuerName>
        <issuerTradingSymbol>VAR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001217439</rptOwnerCik>
            <rptOwnerName>FINNEY ELISHA W</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O VARIAN MEDICAL SYSTEMS</rptOwnerStreet1>
            <rptOwnerStreet2>3100 HANSEN WAY, , MAIL STOP E-327</rptOwnerStreet2>
            <rptOwnerCity>PALO ALTO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94304-1030</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isOfficer>1</isOfficer>
            <officerTitle>SVP, Finance and CFO</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2011-11-04</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>39.85</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>47995</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Non-qualified Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>39.85</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2011-11-04</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness></transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-11-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>10000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>43000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The amended Form 4 is being filed to correctly disclose the price of the shares acquired from the exercise of stock options.  The original Form 4 incorrectly disclosed that the price was $0, whereas the shares were actually acquired from exercising of stock options with an option price of $39.85 per share.</footnote>
        <footnote id="F2">Stock option granted under the Varian Medical Systems, Inc. Omnibus Stock Plan, which complies with new Rule 16b-3.  The option vests as follows: one third on 11/18/05, and the remaining shares in 24 equal installments over the 24 months following the first vesting date.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Franco N. Palomba, Attorney in Fact for Elisha W. Finney</signatureName>
        <signatureDate>2011-11-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
