<PAGE>   1

                                  UNITED STATES

                       SECURITIES AND EXCHANGE COMMISSION

                             Washington, D.C. 20549


                               FORM 10-K/A No. 2


              ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                         SECURITIES EXCHANGE ACT OF 1934
                        For The Year Ended June 30, 2001

                         Commission File Number: 0-26802

                              CHECKFREE CORPORATION

             (Exact name of Registrant as specified in its charter)

              DELAWARE                                     58-2360335
   (State or other jurisdiction of                      (I.R.S. Employer
   incorporation or organization)                      Identification No.)

                           4411 EAST JONES BRIDGE ROAD
                             NORCROSS, GEORGIA 30092
                    (Address of principal executive offices,
                               including zip code)

                                 (678) 375-3000
                         (Registrant's telephone number,
                              including area code)

Securities registered pursuant to
Section 12(b) of the Act:                    None

Securities registered pursuant to
Section 12(g) of the Act:                    Common Stock, $.01 par value
                                             Preferred Stock Purchase Rights

     Indicate by check mark whether the Registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
Registrant was required to file such reports), and (2) has been subject to the
filing requirements for at least the past 90 days. Yes   X    No
                                                       ----      ----

         Indicate by check mark if disclosure of delinquent filers pursuant to
Item 405 of Regulation S-K is not contained herein, and will not be contained,
to the best of registrant's knowledge, in definitive proxy or information
statements incorporated by reference in Part III of this Form 10-K or any
amendment to this Form 10-K. [ ]

         The aggregate market value of our Common Stock held by our
non-affiliates was approximately $1,050,442,170 on September 14, 2001.

         There were 87,154,357 shares of our Common Stock outstanding on
September 14, 2001.

                       DOCUMENTS INCORPORATED BY REFERENCE

         Portions of our Annual Report to Stockholders for the fiscal year ended
June 30, 2001 are incorporated by reference in Part II.

         Portions of our Proxy Statement for the 2001 Annual Meeting of
Stockholders are incorporated by reference in Part III.


<PAGE>   2


                          AMENDMENT NO. 2 TO FORM 10-K

         This amendment no. 2 to Form 10-K is being filed as a filing error was
made relating to Exhibit 13. A revised Exhibit 13 is attached hereto in its
entirety.

<PAGE>   3

                                   SIGNATURES

         Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, we have duly caused this report to be signed on its behalf
by the undersigned, thereunto duly authorized.

                                   CHECKFREE CORPORATION


Date: October 4, 2001              By:   /s/ DAVID E. MANGUM
                                      -----------------------------------------
                                         David E. Mangum, Executive Vice
                                         President and Chief Financial
                                         Officer



         Pursuant to the requirements of the Securities Exchange Act of 1934,
this report has been signed below by the following persons on our behalf and in
the capacities indicated on the 4th day of October, 2001.


<TABLE>
<CAPTION>

            Signature                                          Title
<S>                                          <C>
        *Peter J. Kight                      Chairman of the Board and Chief Executive Officer
----------------------------------------     (Principal Executive Officer)
         Peter J. Kight


        *David E. Mangum                     Executive Vice President and Chief
----------------------------------------     Financial Officer
         David E. Mangum                     (Principal Financial Officer)


        *Gary A. Luoma, Jr.                  Senior Vice President and Chief Accounting
----------------------------------------     Officer
         Gary A. Luoma, Jr.                  (Principal Accounting Officer)


        *William P. Boardman                 Director
---------------------------------------
         William P. Boardman

        *James D. Dixon                      Director
----------------------------------------
         James D. Dixon

        *Henry C. Duques                     Director
----------------------------------------
         Henry C. Duques

        *Mark A. Johnson                     Director
---------------------------------------
         Mark A. Johnson

        *Lewis C. Levin                      Director
---------------------------------------
         Lewis C. Levin

        *Eugene F. Quinn                     Director
---------------------------------------
         Eugene F. Quinn

        *Jeffrey M. Wilkins                  Director
---------------------------------------
         Jeffrey M. Wilkins

*By: /s/ Curtis A. Loveland
    -----------------------------------
         Curtis A. Loveland,
         Attorney-in-Fact
</TABLE>


                                      -42-