<PAGE>   1
                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                   FORM 10-Q

(Mark One)

[ X ]    QUARTERLY REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES
         EXCHANGE ACT OF 1934

For the quarterly period ended December 31, 1996

                                       OR

[   ]    TRANSITION REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
         ACT OF 1934

For the transition period from                           to


                        Commission file number: 0-26802

                             CHECKFREE CORPORATION
             (Exact name of registrant as specified in its charter)

           DELAWARE                                             31-1013521
(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)

                                 (770) 441-3387
              (Registrant's telephone number, including area code)

                                 NOT APPLICABLE
              (Former name, former address and former fiscal year,
                         if changed since last report)

         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 the number of shares outstanding of each of the registrant's
classes of common stock, as of the latest practicable date: 54,283,237 shares
of Common Stock, $.01 par value, were outstanding at January 28, 1997.


<PAGE>   2

                                   FORM 10-Q

                             CHECKFREE CORPORATION

                               TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                                                                                 PAGE NO.
<S>     <C>                                                                                        <C>
PART I.       FINANCIAL INFORMATION

         Item 1.      Financial Statements.

                      Condensed Consolidated Balance Sheets                                          3
                           June 30, 1996 and December 31, 1996

                      Condensed Consolidated Statements of                                           4
                           Operations For the Three Months and Six
                           Months Ended December 31, 1995 and 1996

                      Condensed Consolidated Statements of                                           5
                           Cash Flows For the Three Months and Six
                           Months Ended December 31, 1995 and 1996

                      Notes to Interim Condensed Consolidated Unaudited                              6
                            Financial Statements For the Three Months
                           and Six Months Ended December 31, 1995 and 1996

         Item 2.      Management's Discussion and Analysis of Financial
                      Condition and Results of Operations.                                         7-11

PART II.      OTHER INFORMATION

         Item 1.      Legal Proceedings.                                                            N/A

         Item 2.      Changes in Securities.                                                        N/A

         Item 3.      Defaults Upon Senior Securities.                                              N/A

         Item 4.      Submission of Matters to a Vote of Security Holders.                          N/A

         Item 5.      Other Information.                                                            12

         Item 6.      Exhibits and Reports on Form 8-K.                                            13-15

         Signatures                                                                                 16
</TABLE>

                                      -2-

<PAGE>   3


                         PART 1. FINANCIAL INFORMATION

ITEM 1.   FINANCIAL STATEMENTS

                     CHECKFREE CORPORATION AND SUBSIDIARIES
                     CONDENSED CONSOLIDATED BALANCE SHEETS

<TABLE>
<CAPTION>
                                                                                June 30,                   December 31,
                                                                                  1996                         1996        
                                                                          --------------------          -------------------
                                    ASSETS                                                                  (Unaudited)
<S>                                                                       <C>                           <C>
Current Assets:
  Cash and cash equivalents                                                       $ 20,987,355                 $ 29,466,280
  Investments                                                                       18,089,029                   10,873,193
  Accounts receivable, net                                                          29,591,417                   27,183,287
  Assets held for sale                                                              20,000,000                           --
  Prepaid expenses and other                                                         2,205,026                    3,561,715
                                                                          --------------------          -------------------
      Total Current Assets                                                          90,872,827                   71,084,475

Property and equipment, net                                                         36,567,141                   35,675,608
Capitalized software, net                                                           37,107,680                   35,742,573
Intangible assets, net                                                              27,507,677                   26,124,459
Investments and other assets                                                         4,174,219                    3,870,995
                                                                          --------------------          -------------------

Total                                                                            $ 196,229,544                 $172,498,110
                                                                          ====================          ===================

                  LIABILITIES AND STOCKHOLDERS' EQUITY
Current Liabilities:
  Accounts payable                                                                   5,139,607                    4,182,431
  Accrued liabilities                                                               16,038,095                   15,062,109
  Current portion of long-term obligations                                           1,112,184                    1,008,218
  Deferred revenues                                                                 15,388,797                   18,863,165
  Deferred income taxes                                                              7,819,505                    5,525,460
                                                                          --------------------          -------------------
      Total Current Liabilities                                                     45,498,188                   44,641,383


Deferred income taxes                                                                4,732,324                           --
Long-term obligations - less current portion                                         8,324,317                    8,222,606
                                                                          --------------------          -------------------
      Total Liabilities                                                             58,554,829                   52,863,989
                                                                          --------------------          -------------------

Stockholders' Equity:
  Preferred stock - 15,000,000 authorized shares, $.01 par value; 
      no shares issued or outstanding                                                      --                           --
  Common stock - 150,000,000 authorized shares, $.01 par value;
      42,274,800 and 42,542,913 shares issued                                          422,748                      425,429
  Additional paid in capital                                                       276,823,109                  277,082,991
  Treasury stock - at cost, 757,536 and 1,034,005 shares                              (629,481)                  (5,882,392)
  Accumulated deficit                                                             (138,941,661)                (151,991,907)
                                                                          --------------------          ------------------- 
      Total Stockholders' Equity                                                   137,674,715                  119,634,121
                                                                          --------------------          -------------------

  Total                                                                           $196,229,544                 $172,498,110
                                                                          ====================           ==================
</TABLE>

   See Notes to Interim Condensed Consolidated Unaudited Financial Statements

                                      -3-

<PAGE>   4


                     CHECKFREE CORPORATION AND SUBSIDIARIES
                CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                             Three months ended December 31,           Six months ended December 31,    
                                           -----------------------------------      ------------------------------------
                                                1995                1996                 1995                 1996      
                                           --------------      ---------------      ---------------      ---------------
<S>                                           <C>                 <C>                <C>                  <C>
Revenues:
  Processing and servicing                    $10,818,012          $17,795,490          $20,645,280          $35,731,896
  Merchant discount                             2,608,108            3,382,568            5,103,394            6,633,023
  License                                              --            8,602,294                   --           13,494,148
  Maintenance                                          --            4,766,173                   --            8,353,019
  Other                                                --            3,958,501                   --            6,954,805
                                           --------------      ---------------      ---------------      ---------------
      Total revenues                           13,426,120           38,505,026           25,748,674           71,166,891
                                           --------------      ---------------      ---------------      ---------------

Expenses:                                                                                                               
  Cost of processing, servicing and support     8,355,792           23,021,538           15,797,461           44,824,375
  Research and development                      1,962,730            7,013,834            3,856,956           13,968,225
  Sales and marketing                           2,442,838            6,849,083            4,182,083           12,409,935
  General and administrative                    1,203,120            4,559,814            2,218,764            9,605,532
  Depreciation and amortization                   655,566            5,755,731            1,291,050           11,316,541
                                           --------------      ---------------      ---------------      ---------------
      Total expenses                           14,620,046           47,200,000           27,346,314           92,124,608
                                           --------------      ---------------      ---------------      ---------------

Loss from operations                           (1,193,926)          (8,694,974)          (1,597,640)         (20,957,717)

Interest, net                                   1,186,992              511,344            1,285,576              882,375
                                           --------------      ---------------      ---------------      ---------------

Loss before income taxes                           (6,934)          (8,183,630)            (312,064)         (20,075,342)

Income tax expense (benefit)                      115,716           (2,862,996)             (21,592)          (7,025,096)
                                           --------------      ---------------      ---------------      --------------- 

Net loss                                   $     (122,650)       $ (5,320,634)       $    (290,472)      $  (13,050,246)
                                           ==============      ===============      ===============      ===============

Net loss per common share                  $       (0.00)        $      (0.13)      $        (0.01)      $        (0.31)
                                           =============       ==============       ==============       ==============

Weighted average common shares outstanding    31,888,510           41,533,981           29,535,719           41,582,074
                                           =============       ==============       ==============       ==============      
</TABLE>


   See Notes to Interim Condensed Consolidated Unaudited Financial Statements

                                      -4-

<PAGE>   5

                     CHECKFREE CORPORATION AND SUBSIDIARIES
                CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                                                                     Six Months Ended December 31,        
                                                                              --------------------------------------------
                                                                                     1995                     1996        
                                                                              -------------------     --------------------
<S>                                                                               <C>                      <C>
Cash flows from operating activities:
  Net loss                                                                          $    (290,472)           $ (13,050,246)
  Adjustments to reconcile net loss to net cash provided by (used in) 
      operating activities:
      Depreciation and amortization                                                     1,291,050               11,316,541
      Deferred income taxes                                                                78,628               (7,026,369)
      Gain on sale of business                                                                 --                 (213,132)
      Loss on disposal of property and equipment                                           11,650                  262,811
      Change in certain assets and liabilities:
        Accounts receivable, net                                                       (1,105,803)               2,408,130
        Prepaid expenses and other                                                       (623,262)              (1,249,860)
        Accounts payable                                                                  535,240                 (957,176)
        Accrued liabilities                                                               730,729                 (975,986)
        Deferred revenues                                                                  (1,733)               3,474,368
                                                                              -------------------     --------------------
           Net cash provided by (used in) operating activities                            626,027               (6,010,919)
                                                                              -------------------     -------------------- 

Cash flows from investing activities:
  Purchase of property and software                                                    (5,205,172)              (7,893,171)
  Proceeds from the sale of property and equipment                                            100                  352,999
  Proceeds from sale of business                                                               --               19,000,000
  Proceeds from maturities and sales of investments                                    37,725,000               13,231,688
  Purchase of investments                                                             (55,409,194)              (4,517,345)
                                                                              -------------------     -------------------- 
           Net cash provided by (used in) investing activities                        (22,889,266)              20,174,171
                                                                              -------------------     --------------------

Cash flows from financing activities:
  Proceeds from sales of common stock, net of expenses                                 82,698,642                       --
  Repayment of notes payable and other debt extinguishment                                (37,500)                 (31,250)
  Repayment of stockholders' notes                                                             --                  (50,000)
  Principal payments under capital lease obligations                                     (524,847)                (612,729)
  Proceeds from stock options exercised including related income tax benefits             232,371                  262,563
  Cash payments in lieu of fractional shares                                                 (398)                      --
  Purchase of treasury stock                                                                   --               (5,252,911)
  Payments received on stockholder notes receivable                                       192,139                       --
                                                                              -------------------     --------------------
           Net cash provided by (used in) financing activities                         82,560,407               (5,684,327)
                                                                              -------------------     -------------------- 

Net increase in cash and cash equivalents                                              60,297,168                8,478,925
Cash and cash equivalents at beginning of period                                        3,542,686               20,987,355
                                                                              -------------------     --------------------

Cash and cash equivalents at end of period                                        $    63,839,854          $    29,466,280
                                                                              ===================     ====================

Supplemental disclosure of cash flow information:
  Interest paid                                                                   $       315,101          $       323,524
                                                                              ===================     ====================

Supplemental disclosure of non-cash investing and financing activities:
  Capital lease additions                                                         $       135,769          $       488,302
                                                                              ===================     ====================
</TABLE>

   See Notes to Interim Condensed Consolidated Unaudited Financial Statements

                                      -5-

<PAGE>   6

                     CHECKFREE CORPORATION AND SUBSIDIARIES
     NOTES TO INTERIM CONDENSED CONSOLIDATED UNAUDITED FINANCIAL STATEMENTS
      FOR THE THREE MONTHS AND SIX MONTHS ENDED DECEMBER 31, 1995 AND 1996

         1. The accompanying condensed consolidated financial statements and
notes thereto have been prepared in accordance with the rules and regulations
of the Securities and Exchange Commission for Form 10-Q and include all of the
information and disclosures required by generally accepted accounting
principles for interim financial reporting for Checkfree Corporation and
subsidiaries (the "Company"). The results of operations for the three months
and six months ended December 31, 1995 and 1996 are not necessarily indicative
of the results for the full year.

            These financial statements should be read in conjunction with the
financial statements, accounting policies and financial notes thereto included
in the Company's Transition Report filed with the Securities and Exchange
Commission on Form 10-K/A No. 1. In the opinion of management, the accompanying
condensed consolidated unaudited financial statements reflect all adjustments
(consisting only of normal recurring adjustments) which are necessary for a
fair presentation of financial results for the interim periods presented.

         2. In August 1996, the Company signed a definitive agreement to sell
certain software for $20 million. The sale closed on October 1, 1996 with $19.0
million received at the closing and $1.0 million to be received in 18 months.
The gain on the sale of $213,000 was recognized in the fiscal quarter ended
December 31, 1996.

            On September 15, 1996, the Company entered into a definitive
agreement to purchase Intuit Services Corporation ("ISC"), a wholly owned
subsidiary of Intuit Inc., in exchange for approximately 12.6 million shares of
the Company's common stock. The agreement contains certain provisions that
limit the purchase of additional shares of common stock and the disposition of
shares of common stock to be obtained by Intuit Inc. The acquisition of ISC
closed on January 27, 1997 and will be accounted for under the purchase method
of accounting and is expected to include a charge for in-process research and
development, currently estimated at $120 million. ISC provides transaction
processing and electronic funds transfer services.

            The Company also entered into a Service and License Agreement with
Intuit Inc., whereby the Company will obtain a license to connect to and use
certain software technology of Intuit Inc. for a payment of $10 million on the
closing of the ISC acquisition and $10 million on October 1, 1997.

         3. In the quarter ended December 31, 1996, the Company accrued $1.3
million in personnel benefits related to a realignment of certain customer care
and programming operations. The charge was included in general and
administrative expenses and will affect approximately 60 associates. To date,
no associates have been terminated and no benefits have been paid against the
liability.

         4. Certain amounts in the June 30, 1996 balance sheet have been
reclassified to conform with the December 31, 1996 presentation. In addition,
certain amounts in the condensed consolidated statements of operations for the
three and six months ended December 31, 1995 have been reclassified to conform
with the December 31, 1996 presentation.

                                      -6-

<PAGE>   7

ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
        OF OPERATIONS.

OVERVIEW

As used in this report, "Checkfree" is generally used to indicate Checkfree
Corporation prior to its acquisition of Servantis Systems Holdings, Inc. on
February 21, 1996 (the "Servantis Acquisition"), prior to its acquisition of
Security APL, Inc. on May 9, 1996 (the "Security APL Acquisition"), and prior
to its acquisition of Intuit Services Corporation on January 27, 1997 (the "ISC
Acquisition") (the Servantis Acquisition, the Security APL Acquisition, and the
ISC Acquisition are collectively referred to as the "Acquisitions").
"Servantis" is generally used to indicate Servantis Systems Holdings, Inc.
prior to its acquisition by Checkfree, "Security APL" is generally used to
indicate Security APL, Inc. prior to its acquisition by Checkfree, "ISC" is
generally used to indicate Intuit Services Corporation prior to its acquisition
by Checkfree, and the term the "Company" is used to indicate the combined
company following the Acquisitions. This report contains forward-looking
statements which involve risks and uncertainties. The Company's actual results
may differ materially from the results discussed in the forward-looking
statements. Factors that might cause such a difference include, but are not
limited to, those discussed in "Business -- Business Risks" in the Company's
Transition Report on Form 10-K/A No. 1.

         The Acquisitions further Checkfree's strategy of providing an
expanding range of convenient, secure and cost-effective electronic commerce
services and related products to financial institutions and businesses and
their customers.  Servantis' experience as a provider of electronic commerce
and financial applications software and services to financial institutions
substantially enhances the Company's presence in the financial institutions
market of the electronic commerce segment. Security APL's experience as a
vendor of portfolio management and software services to institutional
investment managers and investment services to consumers enhances the Company's
presence in the consumer and financial institutions market of the electronic
commerce segment. ISC's base of financial institution customers furthers the
Company's home banking and bill payment offering. The integration of
Checkfree's electronic transaction processing and remote delivery technology
with Servantis' software products and market presence, Security APL's portfolio
management and software services, and ISC's financial institution market share
has created a single vendor of electronic commerce services and related
products to an expanded customer base of financial institutions and businesses
and their customers.

         The Company expects to incur operating losses for the next several
quarters. The acquisition of ISC is expected to increase the operating loss for
the quarter ending March 31, 1997. However, with the Company's continued
increase in sales and marketing efforts to promote the Company's new electronic
commerce offerings, and with the continued acceptance in the marketplace of
electronic commerce services, and resulting growth in subscribers, the Company
expects revenues to continue to increase with operating results beginning to
improve in the quarter ending June 30, 1997. The Company intends to increase
research and development costs for new products and services, including the
integration of the products and services of Checkfree, Servantis, Security APL,
and ISC. 

                                      -7-

<PAGE>   8

         The Company expects that these initiatives will allow it to maintain
and enhance its leading position in the rapidly growing electronic commerce
market. There can be no assurance, however, that the Company will be able to
successfully compete against current or future competitors or that the
competitive pressures faced by the Company will not have a material adverse
effect on its business, operating results, and financial condition.

         RESULTS OF OPERATIONS

         The following table sets forth as percentages of total operating
revenues certain consolidated statements of operations' data:

<TABLE>
<CAPTION>
                                             Three months ended December 31,           Six months ended December 31,    
                                           -----------------------------------      ------------------------------------
                                                1995                1996                 1995                 1996      
                                           --------------      ---------------      ---------------      ---------------
<S>                                                 <C>                  <C>                  <C>                  <C>
Total revenues                                      100.0%               100.0%               100.0%               100.0%
                                           --------------      ---------------      ---------------      --------------- 

Expenses:
   Cost of processing, servicing and support         62.2%                59.8%                61.4%                63.0%
   Research and development                          14.6%                18.2%                15.0%                19.6%
   Sales and marketing                               18.2%                17.8%                16.2%                17.4%
   General and administrative                         9.0%                11.9%                 8.6%                13.5%
   Depreciation and amortization                      4.9%                14.9%                 5.0%                15.9%
                                           --------------      ---------------      ---------------      ---------------   
     Total expenses                                 108.9%               122.6%               106.2%               129.4%
                                           --------------      ---------------      ---------------      ---------------   

Loss from operations                                 (8.9)%              (22.6)%               (6.2)%              (29.4)%

Interest, net                                         8.8%                 1.3%                 5.0%                 1.2%
                                           --------------      ---------------      ---------------      ---------------   

Loss before income taxes                             (0.1)%              (21.3)%               (1.2)%              (28.2)%

Income tax expense (benefit)                          1.0%                (7.5)%               (0.1)%               (9.9)%
                                           --------------      ---------------      ---------------      ---------------    

Net loss                                             (0.9)%              (13.8)%               (1.1)%              (18.3)%
                                           ==============      ===============      ===============      ===============    
</TABLE>

         Revenues are reduced by purchased profits of $1.7 million and $7.6
million for the three months and the six months ended December 31, 1996,
respectively. Purchased profits are the estimated profits in deferred revenues
at the Servantis Acquisition date, which were eliminated as a purchase
accounting adjustment. Excluding the purchased profits adjustment, revenues
increased 199% to $40.2 million and 206% to $78.8 million for the three months 
and the six months ended December 31, 1996, respectively. The increases were
primarily due to the acquisitions of Servantis and Security APL, and to a lesser
extent to the internal growth of the Company.

         Costs of processing, servicing and support as a percentage of servicing
revenue (all revenue except licensing fees) and excluding the purchased profits
adjustment were 62.2% and 72.8% for the three months ended December 31, 1995 and
1996, respectively, and 61.4% and 68.7% for the six months ended December 31,
1995 and 1996, respectively. Processing, servicing and support costs increased
as a percentage of servicing revenue for the quarter and year-to-date, due
primarily to an approximate 15% decrease in the average revenue per customer 
for the Company's home banking and bill payment services. The decrease in the 
average revenue per customer is a result of the Company's change in marketing 
strategy in mid-1996 to distribute its bill payment services on a wholesale 
basis through financial institutions. 


                                      -8-

<PAGE>   9

Additionally, the Company has increased its implementation staff to service the
increasing number of financial institutions which have contracted for the
Company's home banking and bill payment offerings.  During the implementation
period, the margin on the implementation revenue is lower than the margin on the
processing revenue.

         Research and development expenses as a percentage of revenues excluding
the purchased profits adjustment were 14.6% and 17.4% for the three months ended
December 31, 1995 and 1996, respectively, and 15.0% and 17.7% for the six months
ended December 31, 1995 and 1996, respectively. The increases as a percentage of
revenue were due to increased product and business development for new and
existing services and related products, including electronic bill presentment
and expanded business and home banking and bill payment offerings, such as
Web-based bill payment.

         Sales and marketing expenses as a percentage of revenues excluding the
purchased profits adjustment were 18.2% and 17.0% for the three months ended
December 31, 1995 and 1996, respectively, and 16.2% and 15.8% for the six months
ended December 31, 1995 and 1996, respectively. The decreases as a percentage of
revenue were primarily due to the increase in revenues and efficiencies gained
from combining the entities.

         General and administrative expenses as a percentage of revenues
excluding the purchased profits adjustment were 9.0% and 11.3% for the three
months ended December 31, 1995 and 1996, respectively, and 8.6% and 12.2% for
the six months ended December 31, 1995 and 1996, respectively. The increases as 
a percentage of revenue were due to higher general and administrative cost from 
the acquired companies, charges for certain disputed accounts receivable, and 
costs of personnel benefits associated with the realignment of certain 
customer care and programming operations in the three months ended December 31,
1996. 

         Depreciation and amortization expenses as a percentage of revenues
excluding the purchased profits adjustment were 4.9% and 14.3% for the three
months ended December 31, 1995 and 1996, respectively, and 5.0% and 14.4% for
the six months ended December 31, 1995 and 1996, respectively. The increases as
a percentage of revenue were primarily due to depreciation and amortization from
the acquired companies for the three and six months ended December 31, 1995 and
1996. Included in depreciation and amortization expense is purchased software
amortization of $2.0 million and $4.0 million for the three month and six month
periods ended December 31, 1996, respectively, which relates solely to license
fee revenue.

         Net interest income decreased by $676,000 and $403,000 for the three
months and the six months ended December 31, 1996, respectively, compared to
the same periods in 1995, due to lower cash, cash equivalent and investment
balances in 1996 compared to 1995. Such cash was used for acquisitions and to
fund operating activities.

                                      -9-

<PAGE>   10

         For the three months and six months ended December 31, 1995, the
Company recognized a $116,000 income tax expense, on a pre-tax loss of $7,000
and a (6.9%) benefit, respectively. For the three months and six
months ended December 31, 1996, the effective income tax rate (benefit) was
(35.0%). The three month and six month period effective tax rates vary from the 
statutory tax rate due to non-deductible items such as meals and entertainment 
and amortization.

LIQUIDITY AND CAPITAL RESOURCES

         For the six months ended December 31, 1996, the Company's operating
activities used cash of $6.0 million. During the six month period, the Company
invested $7.9 million in property and software additions, primarily for
computer related equipment and software and facilities and paid $5.2 million to
purchase treasury stock in conjunction with a put option granted to certain
stockholders in an acquisition. The Company used cash on hand, the net proceeds
from the sale of investments of $8.7 million, as well as the $19.0 million
proceeds from the sale of certain software to finance these operating and
investing activities.

         At December 31, 1996, the Company's cash and cash equivalents and
investments were $41.7 million, a decrease of $200,000 from June 30, 1996. As
of December 31, 1996 the Company's current ratio was 1.6 to 1, compared to a
current ratio of 2.0 to 1 as of June 30, 1996. In addition, working capital was
$26.4 million and $45.4 million at December 31, 1996 and June 30, 1996,
respectively.

         The Company entered into a Service and License Agreement with Intuit
Inc., which required a $10 million payment upon the closing of the ISC
acquisition and $10 million on October 1, 1997. The Company funded the initial
$10 million payment pursuant to the Services and License Agreement with
available cash and investments. The Company expects to fund the $10 million
payment due on October 1, 1997 pursuant to the Services and License Agreement
with available cash and investments.

         With the acquisition of ISC, the Company expects to incur operating
losses into fiscal 1998. The Company believes the existing cash and cash
equivalents and investments will be sufficient to meet the Company's presently
anticipated operating, working capital and capital expenditure requirements for
the foreseeable future. To the extent that the Company needs additional capital
resources, the Company believes that it will have access to both bank financing
and capital leasing for additional facilities and equipment.

INFLATION

         The Company believes the effects of inflation have not had a
significant impact on the Company's results of operations.

                                      -10-

<PAGE>   11

SAFE HARBOR STATEMENT UNDER THE PRIVATE SECURITIES LITIGATION REFORM ACT OF
1995

         Except for the historical information contained herein, the matters
discussed in this Form 10-Q include forward-looking statements that involve
risks and uncertainties. These forward-looking statements involve risks and 
uncertainties, including without limitation, quarterly fluctuations in 
results, the management of growth, the timely implementation of existing bank 
processing agreements, the ability of the Company to sell its processing 
services to additional banks, the acceptance of the Company's electronic 
banking and bill payment services by financial institutions, businesses and 
their customers, the acceptance of the Company's applications software, 
services and related products by financial institutions, the impact of 
competitive services and products, the Company's ability to efficiently 
integrate recent acquisitions, including ISC, Servantis, and Security APL, the 
effect of any future acquisitions or divestitures, and the timely development 
and acceptance of new electronic commerce services and products, as well as the 
various risks inherent in the Company's business and other risks and 
uncertainties detailed from time to time in the Company's periodic reports 
filed with the Securities and Exchange Commission, including the Transition 
Report on Form 10-K/A No. 1 for the six months ended June 30, 1996, and the 
Company's Proxy Statement for the Special Meeting of Stockholders held on 
January 27, 1997. One or more of these factors have affected, and could in the 
future affect, the Company's business and financial results in future periods 
and could cause actual results to differ materially from plans and projections.


                                      -11-

<PAGE>   12

PART II.  OTHER INFORMATION

ITEM 5. OTHER INFORMATION.

         Beginning with the quarter ended December 31, 1996, the Company has
enhanced the presentation of operating expenses on the Statements of Operations
to separately disclose depreciation and amortization. The Company is presenting
the operating expenses in the enhanced format for the periods presented below
for comparison purposes (all information is unaudited):

<TABLE>
<CAPTION>
                                                    Twelve months ended           Quarter ended           Quarter ended
                                                           June 30,                September 30,           December 31,
                                                             1995                      1995                    1995       
                                                     --------------------      --------------------      -----------------
<S>                                                           <C>                      <C>                    <C>
Expenses:
  Cost of processing, servicing and support                   $26,752,106              $  7,441,669           $  8,355,792
  Research and development                                      5,270,336                 1,894,226              1,962,730
  Sales and marketing                                           5,453,691                 1,739,245              2,442,838
  General and administrative                                    3,215,911                 1,015,644              1,244,865
  Depreciation and amortization                                 2,374,001                   635,484                613,821
  In process research and development                                  --                        --                     --
                                                     --------------------      --------------------      -----------------
      Total expenses                                          $43,066,045               $12,726,268            $14,620,046
                                                     ====================      ====================      =================
</TABLE>


<TABLE>
<CAPTION>
                                                        Quarter ended              Quarter ended           Quarter ended
                                                           March 31,                 June 30,              September 30,
                                                             1996                      1996                    1996       
                                                     --------------------      --------------------      -----------------
<S>                                                         <C>                         <C>                    <C>
Expenses:
  Cost of processing, servicing and support                  $ 12,351,769               $23,086,735            $21,802,533
  Research and development                                      4,719,572                 5,187,740              6,954,934
  Sales and marketing                                           6,894,229                10,272,928              5,560,792
  General and administrative                                    3,351,170                 3,986,505              5,045,584
  Depreciation and amortization                                 1,918,958                 5,078,143              5,560,810
  In process research and development                          93,757,586                28,600,000                     --
                                                     --------------------      --------------------      -----------------
      Total expenses                                         $122,993,284               $76,212,051            $44,924,653
                                                     ====================      ====================      =================
</TABLE>

                                      -12-

<PAGE>   13

ITEM 6.           EXHIBITS AND REPORTS ON FORM 8-K.

         (a)      EXHIBITS.

<TABLE>
<CAPTION>
               EXHIBIT NUMBER                        EXHIBIT DESCRIPTION
                    <S>                 <C>
                    2(a)                Agreement and Plan of Merger, dated as
                                        of September 15, 1996, among the
                                        Registrant, Checkfree Acquisition
                                        Corporation II, Intuit Inc., and Intuit
                                        Services Corporation. (Reference is made
                                        to Exhibit 2 to the Current Report on
                                        Form 8-K, dated September 15, 1996,
                                        filed with the Securities and Exchange
                                        Commission, and incorporated herein by
                                        reference.)

                    2(b)                Amendment No. 1 to Agreement and Plan of
                                        Merger, dated as of September 15, 1996,
                                        among the Registrant, Checkfree
                                        Acquisition Corporation II, Intuit Inc.,
                                        and Intuit Services Corporation
                                        (Reference is made to Appendix A to the
                                        Proxy Statement for the Special Meeting
                                        of Stockholders held on January 27,
                                        1997, filed with the Securities and
                                        Exchange Commission on December 23,
                                        1996, and incorporated herein by
                                        reference.)

                    10(a)               Checkfree Corporation Amended and
                                        Restated 1995 Stock Option Plan.
                                        (Reference is made to Exhibit 10(jjj) to
                                        the Registration Statement on Form S-4
                                        filed with the Securities and Exchange
                                        Commission on October 31, 1996
                                        (Registration No. 333-15247) and
                                        incorporated herein by reference.)

                    10(b)               Checkfree Corporation Associate Stock
                                        Purchase Plan. (Reference is made to
                                        Exhibit 10(kkk) to the Registration
                                        Statement on Form S-4 filed with the
                                        Securities and Exchange Commission on
                                        October 31, 1996 (Registration No.
                                        333-15247) and incorporated herein by
                                        reference.)

                    10(c)               Stockholder Agreement between Intuit
                                        Inc. and Peter J. Kight, as a
                                        shareholder of the Company. (Reference
                                        is made to Exhibit 10(lll) to the
                                        Registration Statement on Form S-4 filed
                                        with the Securities and Exchange
                                        Commission on October 31, 1996
                                        (Registration No. 333-15247) and
                                        incorporated herein by reference.)
</TABLE>

                                      -13-

<PAGE>   14


<TABLE>
                    <S>                 <C>
                    10(d)               Stockholder Agreement between Intuit
                                        Inc. and Mark A. Johnson, as a
                                        shareholder of the Company. (Reference
                                        is made to Exhibit 10(mmm) to the
                                        Registration Statement on Form S-4 filed
                                        with the Securities and Exchange
                                        Commission on October 31, 1996
                                        (Registration No. 333-15247) and
                                        incorporated herein by reference.)

                    10(e)               Stock Restriction Agreement between the
                                        Company and Intuit Inc. (Reference is
                                        made to Exhibit 10(nnn) to the
                                        Registration Statement on Form S-4 filed
                                        with the Securities and Exchange
                                        Commission on October 31, 1996
                                        (Registration No. 333-15247) and
                                        incorporated herein by reference.)

                    10(f)               Form of Escrow Agreement among the
                                        Company, Intuit Inc. and a to be named
                                        Escrow Agent. (Reference is made to
                                        Exhibit 10(ooo) to the Registration
                                        Statement on Form S-4 filed with the
                                        Securities and Exchange Commission on
                                        October 31, 1996 (Registration No.
                                        333-15247) and incorporated herein by
                                        reference.)

                    10(g)               Form of Registration Rights Agreement
                                        between the Company and Intuit Inc.
                                        (Reference is made to Exhibit 10(ppp) to
                                        the Registration Statement on Form S-4
                                        filed with the Securities and Exchange
                                        Commission on October 31, 1996
                                        (Registration No. 333-15247) and
                                        incorporated herein by reference.)

                    10(h)               Services and License Agreement, dated as
                                        of September 15, 1996, between Checkfree
                                        Corporation and Intuit Inc. (Reference
                                        is made to Exhibit 10(a) to the Current
                                        Report on Form 8-K, dated November 22,
                                        1996, filed with the Securities and
                                        Exchange Commission, and incorporated
                                        herein by reference.)**

                    10(i)               Amended and Restated Registration Rights
                                        Agreement, dated as of September 15,
                                        1996, between Checkfree Corporation and
                                        Intuit Inc. (Reference is made to
                                        Exhibit 10(a) to the Current Report on
                                        Form 8-K, dated December 16, 1996, filed
                                        with the Securities and Exchange
                                        Commission, and incorporated herein by
                                        reference.)

                    10(j)               Amended and Restated stock Restriction
                                        Agreement, dated as of September 15,
                                        1996, between Checkfree Corporation and
                                        Intuit Inc. (Reference is made to
                                        Exhibit 10(b) to the Current Report on
                                        Form 8-K, dated December 16, 1996, filed
                                        with the Securities and Exchange
                                        Commission, and incorporated herein by
                                        reference.)
</TABLE>

                                      -14-

<PAGE>   15


<TABLE>
                    <S>         <C>       <C>
                    10(k)       *         Form of Amended Registration Rights
                                          Agreement, dated as of January 27,
                                          1997, between Checkfree and the former
                                          stockholders of Security APL, Inc.

                     27         *         Financial Data Schedule.
</TABLE>

         -------------
         *        Filed with this Report.

         **       The Registrant has requested that portions of this Exhibit be
                  given confidential treatment.

         (b)      REPORTS ON FORM 8-K.

         The Registrant filed the following Current Reports on Form 8-K with
the Securities and Exchange Commission:

                  (i)      A Current Report on Form 8-K, dated as of October 1,
                           1996, was filed with the Securities and Exchange
                           Commission on October 9, 1996 (Items 2 and 7).

                  (ii)     A Current Report on Form 8-K/A No. 2, dated as of
                           May 9, 1996, was filed with the Securities and
                           Exchange Commission on October 11, 1996 
                           (Items 2 and 7).

                  (iii)    A Current Report on Form 8-K, dated as of November
                           22, 1996, was filed with the Securities and Exchange
                           Commission on December 6, 1996 (Items 5 and 7).

                  (iv)     A Current Report on Form 8-K, dated as of December
                           16, 1996, was filed with the Securities and Exchange
                           Commission on December 18, 1996 (Items 5 and 7).

                  (v)      A Current Report on Form 8-K, dated as of January
                           27, 1997, was filed with the Securities and Exchange
                           Commission on January 27, 1997 (Items 2 and 7).

                  (vi)     A Current Report on Form 8-K, dated as of January
                           31, 1997, was filed with the Securities and Exchange
                           Commission on February 3, 1997 (Items 5 and 7).

                                      -15-

<PAGE>   16


                                   SIGNATURES

         Pursuant to the requirements of the Securities Exchange Act of 1934,
the Registrant has duly caused this amended report to be signed on its behalf
by the undersigned thereunto duly authorized.

                                  CHECKFREE CORPORATION

Date:  February 11, 1997          By: /s/ JAMES S. DOUGLASS
                                     -----------------------------------------  
                                         James S. Douglass, Executive Vice
                                         President, Finance and Chief Financial
                                         Officer*
                                         (Principal Financial Officer)

Date:  February 11, 1997          By: /s/ JOHN M. STANTON
                                     ----------------------------------------  
                                         John M. Stanton, Vice President,
                                         Treasurer, and Assistant Secretary
                                         (Principal Accounting Officer)

*    In his capacity as Executive Vice President, Finance and Chief
     Financial Officer, Mr. Douglass is duly authorized to sign this amended
     report on behalf of the Registrant.

                                      -16-

<PAGE>   17





                             CHECKFREE CORPORATION

                        FORM 10-Q FOR THE QUARTER ENDED
                               DECEMBER 31, 1996

                                 EXHIBIT INDEX


<PAGE>   18




<TABLE>
<CAPTION>
      EXHIBIT                                          EXHIBIT                                      EXHIBIT INDEX
      NUMBER                                         DESCRIPTION                                     PAGE NUMBER
       <S>                 <C>
       2(a)                Agreement and Plan of Merger, dated as of September
                           15, 1996, among the Registrant, Checkfree Acquisition
                           Corporation II, Intuit Inc., and Intuit Services
                           Corporation (Reference is made to Exhibit 2 to the
                           Current Report on Form 8-K, dated September 15, 1996,
                           filed with the Securities and Exchange Commission,
                           and incorporated herein by reference.)

       2(b)                Amendment No. 1 to Agreement and Plan of Merger,
                           dated as of September 15, 1996, among the Registrant,
                           Checkfree Acquisition Corporation II, Intuit Inc.,
                           and Intuit Services Corporation (Reference is made to
                           Appendix A to the Proxy Statement for the Special
                           Meeting of Stockholders held on January 27, 1997,
                           filed with the Securities and Exchange Commission on
                           December 23, 1996, and incorporated herein by
                           reference.)

       10(a)               Checkfree Corporation Amended and Restated 1995 Stock
                           Option Plan. (Reference is made to Exhibit 10(jjj) to
                           the Registration Statement on Form S-4 filed with the
                           Securities and Exchange Commission on October 31,
                           1996 (Registration No. 333-15247) and incorporated
                           herein by reference.)

       10(b)               Checkfree Corporation Associate Stock Purchase Plan.
                           (Reference is made to Exhibit 10(kkk) to the
                           Registration Statement on Form S-4 filed with the
                           Securities and Exchange Commission on October 31,
                           1996 (Registration No. 333- 15247) and incorporated
                           herein by reference.)

       10(c)               Stockholder Agreement between Intuit Inc. and Peter
                           J. Kight, as a shareholder of the Company. (Reference
                           is made to Exhibit 10(lll) to the Registration
                           Statement on Form S-4 filed with the Securities and
                           Exchange Commission on October 31, 1996 (Registration
                           No. 333-15247) and incorporated herein by reference.)
</TABLE>


<PAGE>   19

<TABLE>
       <S>                 <C>
       10(d)               Stockholder Agreement between Intuit Inc. and Mark A.
                           Johnson, as a shareholder of the Company. (Reference
                           is made to Exhibit 10(mmm) to the Registration
                           Statement on Form S-4 filed with the Securities and
                           Exchange Commission on October 31, 1996 (Registration
                           No. 333-15247) and incorporated herein by reference.)

       10(e)               Stock Restriction Agreement between the Company and
                           Intuit Inc. (Reference is made to Exhibit 10(nnn) to
                           the Registration Statement on Form S-4 filed with the
                           Securities and Exchange Commission on October 31,
                           1996 (Registration No. 333-15247) and incorporated
                           herein by reference.)

       10(f)               Form of Escrow Agreement among the Company, Intuit
                           Inc. and a to be named Escrow Agent. (Reference is
                           made to Exhibit 10(ooo) to the Registration Statement
                           on Form S-4 filed with the Securities and Exchange
                           Commission on October 31, 1996 (Registration No.
                           333-15247) and incorporated herein by reference.)

       10(g)               Form of Registration Rights Agreement between the
                           Company and Intuit Inc. (Reference is made to Exhibit
                           10(ppp) to the Registration Statement on Form S-4
                           filed with the Securities and Exchange Commission on
                           October 31, 1996 (Registration No. 333-15247) and
                           incorporated herein by reference.)

       10(h)               Services and License Agreement, dated as of September
                           15, 1996, between Checkfree Corporation and Intuit
                           Inc. (Reference is made to Exhibit 10(a) to the
                           Current Report on Form 8-K, dated November 22, 1996,
                           filed with the Securities and Exchange Commission,
                           and incorporated herein by reference.)**

       10(i)               Amended and Restated Registration Rights Agreement,
                           dated as of September 15, 1996, between Checkfree
                           Corporation and Intuit Inc. (Reference is made to
                           Exhibit 10(a) to the Current Report on Form 8-K,
                           dated December 16, 1996, filed with the Securities
                           and Exchange Commission, and incorporated herein by
                           reference.)
</TABLE>

<PAGE>   20

<TABLE>
       <S>        <C>      <C>
       10(j)               Amended and Restated stock Restriction Agreement,
                           dated as of September 15, 1996, between Checkfree
                           Corporation and Intuit Inc. (Reference is made to
                           Exhibit 10(b) to the Current Report on Form 8-K,
                           dated December 16, 1996, filed with the Securities
                           and Exchange Commission, and incorporated herein by
                           reference.)

       10(k)      *        Form of Amended Registration Rights Agreement,
                           dated as of January 27, 1997, between Checkfree and
                           the former stockholders of Security APL, Inc.

        27        *        Financial Data Schedule.
</TABLE>

------------------ 

*   Filed with this Report. 

**  The Registrant has requested that portions of this Exhibit be given 
    confidential treatment.