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

    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2004-03-16</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001034088</issuerCik>
        <issuerName>ECLIPSYS CORP</issuerName>
        <issuerTradingSymbol>ECLP</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001213696</rptOwnerCik>
            <rptOwnerName>PATTON JOHN T JR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>620 NEWPORT CENTER DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2>11TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEWPORT BEACH</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92660</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>1</isOther>
            <officerTitle>Former COO</officerTitle>
            <otherText>Former Executive V.P.</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Common Stock (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.4380</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-03-16</value>
            </transactionDate>
            <deemedExecutionDate>
                <value>2004-03-16</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>23021.0000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>12.5700</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2001-05-26</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2010-05-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>23021.0000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>249885.0000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Common Stock (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.4380</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-03-17</value>
            </transactionDate>
            <deemedExecutionDate>
                <value>2004-03-17</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>25000.0000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>13.2700</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2001-05-26</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2010-05-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>25000.0000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>224885.0000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Option vests 25% on the first anniversary of the grant date (May 26, 2001), and vests monthly thereafter until option fully vests on the fourth anniversary of the grant date (May 26, 2004).</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Brent A. Friedman
Under a Power of Attorney</signatureName>
        <signatureDate>2004-03-18</signatureDate>
    </ownerSignature>
</ownershipDocument>

