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

                                  FORM 10-K/A

                                AMENDMENT NO. 2

[X] ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
    ACT OF 1934

                   FOR THE FISCAL YEAR ENDED DECEMBER 31, 1999

                                       OR

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

                FOR THE TRANSITION PERIOD FROM _______ TO _______

                         COMMISSION FILE NUMBER 0-21031

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

            DELAWARE                                         52-1992861
 (State or other jurisdiction of                          (I.R.S. Employer
 incorporation or organization)                          Identification No.)

                 22 PELICAN WAY, SAN RAFAEL, CALIFORNIA, 94901
          (Address of Principal Executive Offices, including Zip Code)

        Registrant's telephone number, including area code: (415)482-2100

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

           Securities registered pursuant to Section 12(g) of the Act:

                     COMMON STOCK, $0.01 PAR VALUE PER SHARE
                                (Title of Class)

   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 report), and (2) has been subject to such
filing requirements for 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 the registrant's knowledge, in definitive proxy or information
statements incorporated by reference in Part III of this Form 10-K or any
amendment to the Form 10-K. [ ]

   The aggregate market value of voting stock held by non-affiliates of the
Registrant, as of March 31, 2000 was approximately $102,490,363 (based upon the
closing price for shares of the Registrant's Common Stock as reported by the
Nasdaq National Market for the last trading date prior to that date). Shares of
Common Stock held by each officer, director and holder of 5% or more of the
outstanding Common Stock have been excluded in that such persons may be deemed
to be affiliates. This determination of affiliate status is not necessarily a
conclusive determination for other purposes.

   On March 31, 2000, approximately 25,473,688 shares of the Registrant's Common
Stock, $0.01 par value per share, were outstanding.



                                       1
<PAGE>   2
                                 AMENDMENT NO. 2

        The undersigned Registrant hereby amends Items 10, 11, 12 and 13 of
its Annual Report on Form 10-K for the fiscal year ended December 31, 1999 and
files such amended Items herewith. The undersigned Registrant also amends Item
14(c) of its Annual Report on Form 10-K for the fiscal year ended December 31,
1999 by adding Exhibits 10.60, 10.61, 10.62, 10.63, 10.64 and 10.65 which are
described in Item 14(c) and files such exhibits herewith.

                                    PART III

ITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT.

        The following sets forth certain information concerning the Company's
directors as of March 31, 2000:

<TABLE>
<CAPTION>
     NAME                 AGE                      POSITION
     ----                 ---                      --------
<S>                       <C>   <C>
James D. Durham(1).........53   Chairman of the Board and Chief Executive Officer
Albert L. Greene(2)........50   Director
Joan P. Neuscheler(3)......39   Director
Michael J. King(4).........61   Director
E.A. Roskovensky(2)........54   Director
Scott Gross(2).............54   Director
Cornelius T. Ryan(1).......69   Director
</TABLE>

(1)  Term of office expires at the 2002 Annual Meeting of Stockholders.
(2)  Term of office expires at the 2000 Annual Meeting of Stockholders.
(3)  Resigned on April 27, 2000.
(4)  Term of office expires at the 2001 Annual Meeting of Stockholders.

BACKGROUND

     James D. Durham serves as QuadraMed's Chairman of the Board and Chief
Executive Officer. Mr. Durham founded the Company in September 1993 when he
became its President and Chief Executive Officer and a director. In May 1996,
Mr. Durham became Chairman of the Board. From November 1992 to December 1993,
Mr. Durham served as the Chief Executive Officer of Trim Healthcare Systems,
Inc., a reimbursement consulting services company. From April 1992 to April
1993, Mr. Durham served as Chief Executive Officer of Care Partners, Inc., an
accounts receivable processing and funding company cofounded by Mr. Durham. From
February 1986 until its acquisition by Ameritech in February 1992, Mr. Durham
served as President and Chief Executive Officer of Knowledge Data Systems, Inc.,
a health care information systems company. Mr. Durham holds a B.S. with honors
in Industrial Engineering from the University of Florida and an M.B.A. with an
emphasis in Finance from the University of California, Los Angeles and is a
Certified Public Accountant.

     Albert L. Greene has been a director of the Company since May 1997. Mr.
Greene is currently the President and Chief Executive Officer of
HealthCentral.com, an online consumer health information service. Previously,
Mr. Green was the Chief Executive Officer of Sutter Health East Bay, a health
care delivery system and the parent company of Alta Bates Health System, from
June 1996 until September 1998. From May 1990 until March 1998, Mr. Greene
served as the President and Chief Executive Officer of Alta Bates Medical
Center, a 527-bed acute care hospital located in Berkeley, California. From
January 1996 until March 1998, Mr. Greene also served as the President and Chief
Executive Officer of Alta Bates Health System, the parent company of Alta Bates
Medical Center. Mr. Greene has served as an executive in hospital administration
since 1979, most recently as the President of Sinai Samaritan Medical Center in
Milwaukee, Wisconsin from 1988 to 1990. Mr. Greene received a masters of
hospital administration at the University of Michigan, and is presently a
diplomate of the American College of Healthcare Executives and a member of the
American Hospital Association. Mr. Greene is also chair-elect of the California
Healthcare Association, a member of the board of directors of Acuson
Corporation, a manufacturer and provider of medical diagnostic ultrasound
systems, and a member of the board of directors of several other privately held
hospitals and hospital associations.

     Joan P. Neuscheler became a director of the Company in March 1994 and
resigned on April 27, 2000. Ms. Neuscheler has been a general partner of
Tullis-Dickerson Partners, a venture capital firm, since September 1992, and the
President and Chief Financial Officer of Tullis-Dickerson & Co., Inc. since
April 1989. Tullis-Dickerson Partners is the general partner of Tullis-Dickerson
Capital Focus, L.P., a stockholder of the Company. Ms. Neuscheler is also a
director of several privately held companies.

     Michael J. King has been a director of the Company since May 1999. Mr. King
has been the Chief Executive Officer of Healthscribe, Inc. since June 1999.
From September 9, 1996 until May 1999, Mr. King served as Chairman of the Board
of Directors and Chief Executive Officer of The Compucare Company, a healthcare
information systems company which was acquired by QuadraMed in March 1999.
Prior to joining The Compucare Company, Mr. King was Chairman of the Board of
Directors, Chief Executive Officer and President of Software AG of the
Americas, a leader in Enterprise Information Systems. Mr. King previously
served as President and Chief Executive Officer of Computer Entry Systems Corp.
and has held various high-level positions at Marietta Data Systems and the
Hoskyns Group in the United Kingdom. Mr. King holds a degree in Mechanical
Engineering from the University of Sheffield and a M.B.A. equivalent in
Management Studies from the University of Hatfield.

     E.A. Roskovensky has been a director of the Company since May 1999. Mr.
Roskovensky has been the President and Chief Operating Officer of Robertson-Ceco
Corp., a publicly traded company which manufactures custom engineered metal
buildings, since November 1994. Mr. Roskovensky also has been the President and
Chief Executive Officer of Davis Wire Corporation since 1991. Mr. Roskovensky
previously has held positions at USS-Posco Industries, Double Eagle Steel
Coating Company and U.S. Steel. Mr. Roskovensky holds a B.S. in Chemical
Engineering from Villanova University, an M.B.A. from Duquesne University, and a

                                       2
<PAGE>   3

J.D. from the University of Detroit School of Law. He is a member of the State
Bar of Michigan and the Pennsylvania Bar Association.

     Scott Gross has been a director of the Company since March 2000.   Mr.
Gross is currently the founder, President and Chief Executive Officer of Primus
Management, Inc., a successor organization to Alpha Hospital Management, Inc.
where Mr. Gross was the founder, President and Chief Executive Officer from 1989
to 1992.  From 1988 to 1989, Mr. Gross was the Chairman and Chief Executive
Officer of Carondolet Rehabilitation Centers of America, a diversified
rehabilitation medicine services company.  From 1984 to 1987, Mr. Gross was the
President and Chief Executive Officer of Hospital Group - National Medical
Enterprises.  Mr. Gross holds a Bachelor of Science degree in Biology from Cal
State University, Northridge and a  Master degree in Public Administration
(Health Care Management Option ) from the University of Southern California.


     Cornelius T. Ryan has been a director of the Company since March 2000, and
was previously a director of the Company from March 1995 to March 1999.
Mr. Ryan has been a general partner of Oxford Partners since 1981 and of OBP
Management L.P., and OBP Management (Bermuda) Limited Partnership since 1992.
OBP Management L.P. and OBP Management (Bermuda) Limited Partnership are the
general partners of Oxford Bioscience Partners L.P. and Oxford Bioscience
Partners (Bermuda) Limited Partnership, respectively. Mr. Ryan is also a
director of several privately held companies. Mr. Ryan holds a Bachelor of
Commerce in Economics from the University of Ottawa, and an M.B.A. from the
University of Pennsylvania.

                                       3
<PAGE>   4

                                   MANAGEMENT

     The following sets forth the names, ages and positions of the Company's
executive officers and certain key employees as of March 31, 2000:

<TABLE>
<CAPTION>
            NAME              AGE                               POSITION
            ----              ---                               --------
<S>                           <C>   <C>
James D. Durham.............  53    Chairman of the Board and Chief Executive Officer
John V. Cracchiolo..........  43    President, Chief Financial Officer
                                    and Secretary
Keith M. Roberts............  35    Executive Vice President, General Counsel
                                    and Assistant Secretary
Nancy Nelson................  47    Executive Vice President and Chief Operating Officer
Patrick Ahearn..............  45    Executive Vice President, Product Management
Michael Wilstead............  42    Executive Vice President, Sales and Marketing
Randall MacDonald...........  38    Executive Vice President, Customer Services
Andrew Rushmere.............  42    Executive Vice President, Research and Development
Michelle Philpot............  34    Vice President, Finance and Chief Accounting Officer
</TABLE>

BACKGROUND

     John V. Cracchiolo serves as the Company's President, Chief Financial
Officer and Secretary. Mr. Cracchiolo joined the Company in May 1995 as its
Executive Vice President, Chief Financial Officer and Secretary. In May 1998,
he was promoted to President and Chief Operating Officer. Prior to joining the
Company, Mr. Cracchiolo worked for PSICOR, Inc., a health care services
company, serving as its Chief Financial Officer from February 1993 to May 1995,
and its corporate Controller from May 1989 to February 1993. Previously, Mr.
Cracchiolo worked in various management positions for software, hardware,
defense contractor and personnel and professional services organizations within
the health care and other industries. Mr. Cracchiolo holds a B.S. in Business
Administration from California State University, Long Beach and is a Certified
Public Accountant.

     Keith M. Roberts was the Company's Executive Vice President, General
Counsel and Assistant Secretary on March 31, 2000. He resigned in April 2000.
Mr. Roberts joined the Company in March 1997 as Vice President and General
Counsel and became Executive Vice President, General Counsel and Assistant
Secretary in February 1998. Mr. Roberts served as the Company's Chief Financial
Officer from June 1998 to April 1999. From May 1995 to March 1997, Mr. Roberts
was an associate of Brobeck, Phleger & Harrison LLP, a private law firm. From
September 1992 to May 1995,

                                        4
<PAGE>   5
Mr. Roberts was an associate of Hale & Dorr, a private law firm. Mr. Roberts
holds a J.D. from Stanford Law School and a B.A. in Economics and Philosophy
from the University of Rochester.

     Nancy Nelson, Executive Vice President and Chief Operating Officer, joined
the Company in March 1999. Before joining the Company, Ms. Nelson was the Senior
Vice President and Chief Operating Officer of The Compucare Company. From
October 1997 until April 1998, Ms. Nelson was Compucare's Senior Vice President
of Product Marketing. Prior to her employment at The Compucare Company, which
was acquired by QuadraMed in March 1999, Ms. Nelson was a principal at First
Consulting Group, a provider of information technology and other consulting
services to payors, providers and healthcare organizations. Ms. Nelson holds a
B.S. in Biological Sciences/Biochemistry from the University of California and
has completed a graduate internship in Medical Technology at California State
University of Long Beach.

     Patrick Ahearn, Executive Vice President of Product Management, joined the
Company in October 1998. Before joining the Company, Mr. Ahearn was Chief
Financial and Chief Information Officer at the Medical Center at Princeton, New
Jersey, a non-profit teaching integrated delivery network. In addition to his
financial and information system responsibilities, he was involved in the
development of the Medical Center's Physician Hospital Organization (PHO),
Medical Services Organization (MSO), its real estate company and its for-profit
ventures. Prior to his experience at Princeton, Mr. Ahearn worked in New York
City for a CPA firm, Pannell Kerr Forster. His experience was almost exclusively
in the healthcare arena and included both the audit and consulting aspects of
the practice. Mr. Ahearn received a Bachelors of Business Administration from
Iona College, New York.

     Michael Wilstead, Executive Vice President of Sales and Marketing, joined
the Company in July 1998 as Vice President of Sales. Prior to joining QuadraMed,
Mr. Wilstead served as a group president at STERIS Corporation, a world leader
in microbial reduction and surgical support products. Prior to that, he held
positions at AMSCO International and AMSCO Canada, both of which are medical
equipment companies. Mr. Wilstead also founded Rocky Mountain Medical, a durable
medical equipment company, which he sold after six years. Mr. Wilstead holds a
bachelor of science in business administration from the University of Phoenix.

     Randall R. Macdonald serves as Executive Vice President of Customer
Services. Prior to joining QuadraMed in June 1998, Mr. Macdonald held a similar
position at Pyramid Health Group, Inc., a cash flow management services company,
which he joined in February 1998. Prior to that date, Mr. Macdonald held
positions as Manager of Information Technology Management for Nissan Motor
Corporation USA and as a senior manager with Andersen Consulting. Mr. Macdonald
holds a Bachelor of Science degree from San Diego State University. He is a
member of the Project Management Institute.

     Andrew K. Rushmere, Executive Vice President of Research and Development,
joined the Company in January 2000 as Executive Vice President of Research and
Development. Most recently, Mr. Rushmere served as vice president at Superior
Consulting, where he was responsible for strategic marketing as well as business
development opportunities and partnerships. Prior to his tenure at Superior, Mr.
Rushmere served as president of Aviant Information, Inc., a division of
Whittaker Corporation. Mr. Rushmere began his work with Whittaker Corporation as
vice president of XYPlex/Hughes LAN Systems. Mr. Rushmere has also held
positions at Persetel Networks as chief technology officer and strategic
marketing vice president, at Grinaker Networks Systems as national sales
manager, at Quality Assured as president and at Hewlett Packard as senior
technical sales manager. Mr. Rushmere earned a T3 in electrical engineering from
SA Navy and a marketing degree from the College of Marketing in South Africa.

     Michelle Philpot was Vice President of Finance and Chief Accounting Officer
of the Company on March 31, 2000. She resigned in May 2000. Prior to joining
QuadraMed in July 1996, Ms. Philpot held positions as manager of worldwide
reporting and assistant controller for Digidesign, Inc., a developer of audio
editing software and systems. Ms. Philpot also spent four years in the audit
department at PricewaterhouseCoopers. Ms. Philpot holds a bachelor of science
in business from California State University-Sacramento. She is a Certified
Public Accountant.


                                        5

<PAGE>   6
            SECTION 16(a) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

     Section 16(a) of the Securities Exchange Act of 1934, as amended, requires
the Company's directors and executive officers, and persons who own more than
ten percent of a registered class of the Company's equity securities
(collectively, "Insiders"), to file with the Securities and Exchange Commission
initial reports of ownership and reports of changes in ownership of Common Stock
and other equity securities of the Company. Officers, directors and greater than
ten percent stockholders are required by Securities and Exchange Commission
regulation to furnish the Company with copies of all Section 16(a) reports they
file. Based solely on its review of the copies of such forms received by it, or
written representation from certain reporting persons that no Form 5s were
required for those persons, the Company believes that all reporting requirements
under Section 16(a) for the fiscal year ended December 31, 1999 were met in a
timely manner by its directors, executive officers, and greater than ten percent
beneficial owners.

                                       6
<PAGE>   7
ITEM 11. EXECUTIVE COMPENSATION

                 SUMMARY OF CASH AND CERTAIN OTHER COMPENSATION

     The following table sets forth certain information regarding the
compensation earned during the last three fiscal years by (i) the Company's
Chief Executive Officer and (ii) each of the five other most highly compensated
executive officers of the Company serving as such as of the end of the last
fiscal year whose total annual salary and bonus exceeded $100,000, for services
rendered in all capacities to the Company and its subsidiaries. Such individuals
will be hereafter referred to as the "Named Executive Officers."

                           SUMMARY COMPENSATION TABLE

<TABLE>
<CAPTION>
                                        ANNUAL COMPENSATION         LONG-TERM COMPENSATION
                                        --------------------    ------------------------------
                                                                RESTRICTED       SECURITIES
     NAME AND PRINCIPAL        FISCAL                             STOCK          UNDERLYING        ALL OTHER
          POSITION              YEAR     SALARY      BONUS        AWARDS      OPTIONS/WARRANTS    COMPENSATION
     ------------------        ------   --------    --------    ----------    ----------------    ------------
<S>                            <C>      <C>         <C>         <C>           <C>                 <C>
James D. Durham..............   1999    $374,000    $367,307            --        100,000            $60,007(5)
  Chairman of the Board and     1998     275,000     412,500    $1,862,000(3)     300,000             30,021(5)
  Chief Executive Officer       1997     225,000     100,000            --        305,000                 --
John V. Cracchiolo...........   1999     256,000     251,580            --         75,000              3,977(5)
  President                     1998     200,000     210,000       997,500(3)     150,000              2,017(5)
                                1997     159,375(1)  103,000            --        155,000                 --
Keith M. Roberts.............   1999     210,000      84,000            --         35,000                 --
  Executive Vice President      1998     159,375(2)  131,250       498,750(3)      35,000                 --
  Counsel                       1997      98,958(4)   50,000            --        100,000                 --
Nancy Nelson.................   1999     206,000      92,700            --        125,000                 --
  Executive Vice President
  and                           1998     190,000      76,220            --         14,853                 --
  Chief Operating Officer       1997     158,750      55,500            --         34,657                 --
Patrick Ahearn...............   1999     200,000          --            --         20,000                 --
  Executive Vice President      1998      49,134(6)       --            --        100,000                 --
  Product Management
Michael Wilstead.............   1999     182,951      50,000            --         90,000                 --
  Executive Vice President      1998     111,911(7)    3,833            --         10,000                 --
  Sales and Marketing
</TABLE>



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

 (1) Effective August 1997, Mr. Cracchiolo's annual salary was increased from
     $150,000 to $175,000 by the Board of Directors.

 (2) Effective July 1998, Mr. Robert's annual salary was increased from $150,000
     to $175,000 by the Board of Directors.

 (3) In October 1998, each of Mr. Durham, Mr. Cracchiolo and Mr. Roberts was
     awarded a right to receive 112,000, 60,000 and 30,000 shares of Common
     Stock, respectively, under the Company's 1996 Stock Incentive Plan, such
     shares to be issued in October, 2003, without payment from the recipient,
     provided that each such individual remains in the Company's service through
     such date. The amounts shown represent the dollar value of the awards based
     on the market price of the underlying shares of Common Stock on the date of
     the bonus share awards in October 1998. As of the last day of the 1999
     fiscal year, the value of the bonus share awards held by each such
     individual, based on the market price of the underlying shares of Common
     Stock on that date, was the following: Mr. Durham - $976,528; Mr.
     Cracchiolo - $523,140; and Mr. Roberts - $261,570. No dividends are payable
     with respect to the bonus share awards until such time as the underlying
     shares of Common Stock have been issued.

 (4) Represents salary paid from March 1997 through December 1997.

 (5) Represents the cash value benefit of split-dollar life insurance premiums
     paid by the Company. The dollar value was established using the demand loan
     valuation method for the whole life portion of the premium paid by the
     Company, projected on an actuarial basis. See "Employment Agreements;
     Change In Control Arrangements" below.

 (6) Represents salary paid from September 1998 through December 1998.

 (7) Represents salary paid from June 1998 through December 1998. Includes
     $27,200 of relocation expense reimbursement.

                                       7
<PAGE>   8

                       OPTION GRANTS IN LAST FISCAL YEAR

     The following table sets forth information concerning the stock option
grants made to each of the Named Executive Officers during the 1999 fiscal year.
No stock appreciation rights were granted during the 1999 fiscal year to the
Named Executive Officers.

                       OPTION GRANTS IN LAST FISCAL YEAR

<TABLE>
<CAPTION>
                                                             INDIVIDUAL GRANTS                       POTENTIAL
                                            ---------------------------------------------------   REALIZABLE VALUE
                                                         PERCENT OF                              AT ASSUMED ANNUAL
                                                           TOTAL                                   RATES OF STOCK
                                            NUMBER OF     OPTIONS                                PRICE APPRECIATION
                                            SECURITIES   GRANTED TO                                  FOR OPTION
                                            UNDERLYING   EMPLOYEES   EXERCISE OR                      TERM(3)
                                             OPTIONS     IN FISCAL    BASE PRICE   EXPIRATION  --------------------
                   NAME                     GRANTED(1)      1999     PER SHARE(2)     DATE       5%         10%
                   ----                     ----------   ----------  ------------- ---------- ---------  -----------
<S>                                         <C>          <C>         <C>           <C>        <C>        <C>
James D. Durham...........................   100,000      3.9%        $8.3125       5/18/09    $522,769   $1,324,798
John V. Cracchiolo........................    75,000      3.0%         8.3125       5/18/09    $392,076      993,599
Keith M. Roberts..........................    35,000      1.4%         7.3750       12/7/09    $162,333      411,385
Nancy Nelson..............................   100,000      3.9%         8.7500       3/22/09    $550,283    1,394,525
Nancy Nelson..............................    25,000      1.0%         7.3750       12/7/09    $115,952      293,846
Patrick Ahearn............................    20,000      0.8%         8.3125       5/18/09    $104,554      264,960
Michael Wilstead..........................    20,000      0.8%         8.7500       3/22/09    $110,057      296,835
Michael Wilstead..........................    35,000      1.4%         8.3125       5/18/09    $182,969      575,241
Michael Wilstead..........................    35,000      1.4%         7.3750       12/7/09    $162,333      631,022

</TABLE>

(1) Each option set forth in the table above has a maximum term of ten (10)
    years measured from the grant date, subject to earlier termination upon the
    executive officer's termination of service with the Company. Each option
    becomes exercisable for 25% of the option shares upon the optionee's
    completion of one year of service measured from the grant date and becomes
    exercisable for the remaining shares in equal monthly installments
    over the next three years of service thereafter. The option will immediately
    become exercisable for all of the option shares upon an acquisition of the
    Company by merger or asset sale unless the options are assumed by the
    successor corporation.

(2) The exercise price may be paid in cash, in shares of the Company's Common
    Stock valued at fair market value on the exercise date or through a cashless
    purchase procedure involving a same-day sale of the purchased shares. The
    Company may also finance the option exercise by loaning the optionee
    sufficient funds to pay the exercise price for the purchased shares and the
    federal and state income tax liability incurred by the optionee in
    connection with such exercise.

(3) There can be no assurance provided to any executive officer or any other
    holder of the Company's securities that the actual stock price appreciation
    over the 10-year option term will be at the assumed 5% and 10% compounded
    annual rates or at any other defined level. Unless the market price of the
    Common Stock appreciates over the option term, no value will be realized
    from the option grants made to the Named Executive Officers.

Option Exercises and Year-End Values

     No stock appreciation rights were granted during the 1999 fiscal year or
outstanding at the end of such fiscal year. The following table sets forth
certain information with respect to the Named Executive Officers concerning
option exercises during the 1999 fiscal year as well as the number of shares of
QuadraMed's common stock subject to exercisable and unexercisable stock options
which the Named Executive Officers held at the end of the 1999 fiscal year.

                                       8
<PAGE>   9

              AGGREGATED OPTION EXERCISES IN LAST FISCAL YEAR AND
                         FISCAL YEAR-END OPTION VALUES

<TABLE>
<CAPTION>
                                                         NUMBER OF SECURITIES              VALUE OF UNEXERCISED
                       (#) SHARES                       UNDERLYING UNEXERCISED           IN-THE-MONEY OPTIONS AT
                        ACQUIRED                      OPTIONS AT FISCAL YEAR-END            FISCAL YEAR-END(1)
                           ON         ($) VALUE     ------------------------------    ------------------------------
        NAME            EXERCISE     REALIZED(2)    EXERCISABLE    NON-EXERCISABLE    EXERCISABLE    NON-EXERCISABLE
        ----           ----------    -----------    -----------    ---------------    -----------    ---------------
<S>                    <C>           <C>            <C>            <C>                <C>            <C>
James D. Durham......   355,600(3)   $2,622,550(3)    481,345(4)       358,229         $      0         $40,650
John V. Cracchiolo...        --              --       214,896          205,104          198,760          30,488
Keith M. Roberts.....        --              --        70,354           83,626               --          47,040
Nancy Nelson.........        --              --        49,510          125,000          110,061          33,600
Patrick Ahearn.......        --              --        30,251           90,833            5,386           8,130
Michael Wilstead.....        --              --         3,333           96,667               --          61,628
</TABLE>

---------------
(1) Calculated by determining the difference between the fair market value of
    Quadramed's common stock as of December 31, 1999 and the exercise price of
    the option.

(2) Calculated by multiplying the number of shares acquired on exercise by the
    difference between the fair market value of the shares on the date of
    exercise and the exercise price.

(3) Represents 355,600 shares of common stock issued upon exercise of a warrant
    held by Mr. Durham. See "Security Ownership of Certain Beneficial Owners and
    Management."

(4) Includes 134,574 shares of common stock issuable upon exercise of a warrant
    held by Trigon Resources Corporation. See "Security Ownership of Certain
    Beneficial Owners and Management."

                             DIRECTOR REMUNERATION

     The non-employee directors receive one thousand dollars ($1,000) for each
board meeting attended and five hundred dollars ($500) for each committee
meeting attended. Non-employee directors are also reimbursed for their
reasonable expenses incurred in connection with attending board meetings.
Non-employee directors receive periodic option grants under the Automatic
Option Grant Program in effect under the Company's 1996 Plan and are eligible
to receive option grants under the Discretionary Option Grant Program of that
plan. Each of these programs is described below.

 Automatic Option Grant Program

     Under the Automatic Option Grant Program, each individual who is first
elected or appointed as a non-employee Board member receives at the time of such
initial election or appointment an automatic option grant for 10,000 shares of
Common Stock, provided such individual was not previously in the Company's
employ. At each annual stockholders meeting, each individual who is to continue
in service as a non-employee Board member is automatically granted at that
meeting an option to purchase 4,000 shares of Common Stock, provided such
individual has served as a non-employee Board member for at least six (6)
months.

     Each option under the Automatic Option Grant Program has an exercise price
per share equal to 100% of the fair market value per share of Common Stock on
the option grant date and a maximum term of ten (10) years measured from the
grant date. The option is immediately exercisable for all the option shares, but
any purchased shares are subject to repurchase by the Company, at the exercise
price paid per share, upon the optionee's cessation of Board service prior to
vesting in those shares. Each initial 10,000-share grant vests, and the
Company's repurchase right lapses, as follows: (i) one-third (1/3) of the option
shares vest upon the optionee's completion of one (1) year of Board service
measured from the option grant date and (ii) the balance of the option shares
vest in a series of twenty-four (24) successive equal monthly installments upon
the optionee's completion of each additional month of Board service over the
twenty-four (24)-month period measured from the first anniversary of such grant
date. Each annual 4,000-share grant vests, and the Company's repurchase right
lapses, in a series of twelve (12) successive equal monthly installments over
the optionee's period of Board service measured from the grant date.

     Mr. Gross received an option for 10,000 shares upon his appointment to the
Board in March 2000, at an exercise price of $5 per share. Mr. Ryan received an
option for 10,000 shares upon his re-appointment to the Board in March 2000, at
an exercise price of $5 per share. On the date of the 2000 Annual Meeting, each
continuing Board member will receive an option for 4,000 shares at an exercise
price per share equal to the fair market value on that date.

Discretionary Option Grant Program

     Under the Discretionary Option Grant Program, eligible individuals in the
Company's employ or service (including non-employee Board members, officers and
consultants) may, at the discretion of the Compensation Committee of the Board,
as Plan Administrator, be granted options to purchase shares of Common Stock at
an exercise price not less than 100% of their fair market value on the grant
date. The Compensation Committee has complete discretion to determine the
vesting schedule, maximum term and the status under Federal tax laws of any such
option grant. No non-employee Board member received any option grants under the
Discretionary Option Grant Program during the 1999 fiscal year.

             EMPLOYMENT AGREEMENTS; CHANGE IN CONTROL ARRANGEMENTS

     In April 1999, the Company entered into a letter agreement with Patrick
Ahearn, Executive Vice President of Product Management. Pursuant to the letter
agreement, Mr. Ahearn is to receive a base salary of $200,000 for the 2000
calendar year and is eligible for such annual cash bonuses as the Board of
Directors in its discretion shall award. The letter agreement also contains the
following severance provisions: (i) if Mr. Ahearn dies, his estate will receive
a special termination payment equal to one months' salary and (ii) if Mr. Ahearn
is terminated by reason of disability or an Involuntary Termination other than a
Termination for Cause (as those terms are defined in the letter agreement), Mr.
Ahearn will receive an aggregate amount equal to his then current annual rate of
base salary and will also continue to receive for a period of 12 months his
life, health and disability and other benefits. In addition, upon a Change in
Control or an Involuntary Termination other than a Termination for Cause, Mr.
Ahearn's outstanding options and all restricted or unvested Common Stock held by
him will vest immediately and remain exercisable for a period of three years
thereafter. The term of the agreement is two years from the effective date and
shall be extended automatically on each succeeding anniversary of the effective
date of the agreement for an additional one (1) year period unless, not later
than three (3) months preceding such anniversary date, the Company shall have
given written notice to Mr. Ahearn that it will not extend the term of the
letter agreement.

     In May 1999, the Company entered into a letter agreement with John V.
Cracchiolo, the Company's President. Pursuant to the letter agreement, Mr.
Cracchiolo is to receive a base salary of $256,000 for the 2000 calendar year
and is eligible for such annual cash bonuses as the Board of Directors in its
discretion shall award. The letter agreement also contains the following
severance provisions: (i) if Mr. Cracchiolo dies, his estate will receive a
special termination payment equal to one months' salary and (ii) if Mr.
Cracchiolo is terminated by reason of disability or an Involuntary Termination
other than a Termination for Cause (as those terms are defined in the letter
agreement), Mr. Cracchiolo will receive an aggregate amount equal to the sum of
(a) two times his then current annual rate of base salary and (b) two times his
then current maximum bonus and will also continue to receive for a period of 24
months his life, health and disability and other benefits. In addition, upon a
Change in Control or an Involuntary Termination other than a Termination for
Cause, Mr. Cracchiolo's outstanding options and all restricted or unvested
Common Stock held by him will vest immediately and remain exercisable for the
full term of the option. The term of the agreement is two

                                       9
<PAGE>   10

years from the effective date and shall be extended automatically on each
succeeding anniversary of the effective date of the agreement for an additional
one (1) year period, unless not later than three (3) months preceding such
anniversary date, the Company shall have given written notice to Mr. Cracchiolo
that it will not extend the term of the letter agreement.

     In January 1999, the Company entered into a letter agreement with James D.
Durham, the Company's Chief Executive Officer. Pursuant to the letter agreement,
Mr. Durham is to receive a base salary of $373,000 for the 2000 calendar year.
In addition, Mr. Durham is eligible for such annual cash bonuses as the Board of
Directors in its discretion shall award, based upon the recommendation of the
Board's Compensation Committee. The letter agreement also contains the following
severance provisions: (i) if Mr. Durham dies, his estate will receive a special
termination payment equal to one months' salary and (ii) if Mr. Durham is
terminated by reason of disability or an Involuntary Termination other than a
Termination for Cause (as those terms are defined in the letter agreement), Mr.
Durham will receive an aggregate amount equal to the sum of (a) three times his
then current annual rate of base salary and (b) three times his then current
maximum bonus and will also continue to receive for a period of 24 months his
life, health and disability and other benefits. In addition, upon a Change in
Control or an Involuntary Termination other than a Termination for Cause, Mr.
Durham's outstanding options and all restricted or unvested Common Stock held by
him will vest immediately and remain exercisable for the full term of the
option. The term of the agreement is two years from the effective date and shall
be extended automatically on each succeeding anniversary of the effective date
of the agreement for an additional one (1) year period, unless not later than
three (3) months preceding such anniversary date, the Company shall have given
written notice to Mr. Durham that it will not extend the term of the letter
agreement.

     In April 1999, the Company entered into a letter agreement with Nancy
Nelson, Executive Vice President and Chief Operating Officer. Pursuant to the
letter agreement, Ms. Nelson was to receive a base salary of $206.000. In
January 2000, Ms. Nelson's base salary was increased to $245,000. Ms. Nelson is
also eligible for such annual cash bonuses as the Board of Directors in its
discretion shall award. The letter agreement also contains the following
severance provisions: (i) if Ms. Nelson dies, her estate will receive a special
termination payment equal to one months' salary and (ii) if Ms. Nelson is
terminated by reason of disability or an Involuntary Termination other than a
Termination for Cause (as those terms are defined in the letter agreement), Ms.
Nelson will receive an aggregate amount equal to her then current annual rate of
base salary and will also continue to receive for a period of 12 months her
life, health and disability and other benefits. In addition, upon a Change in
Control or an Involuntary Termination other than a Termination for Cause, Ms.
Nelson's outstanding options and all restricted or unvested Common Stock held by
her will vest immediately and remain exercisable for a period of three years
thereafter. The term of the agreement is two years from the effective date and
shall be extended automatically on each succeeding anniversary of the effective
date of the agreement for an additional one (1) year period unless, not later
than three (3) months preceding such anniversary date, the Company shall have
given written notice to Ms. Nelson that it will not extend the term of the
letter agreement.

     In 1998 the Company entered into split-dollar life insurance agreements
with Messrs. Durham and Cracchiolo pursuant to which the Company agreed to pay
premiums due on life insurance policies for Messrs. Durham and Cracchiolo. Under
the terms of the agreements, the Company is reimbursed for the amount of the
premiums it pays on the policies at such time as the split dollar life insurance
agreements are terminated, the trusts surrender or cancel the policies, or when
death benefit proceeds are paid under the policies. Such repayment has been
secured by the assignment of the policies to the Company as collateral.


                                       10
<PAGE>   11
     In connection with an acquisition of the Company by merger or asset sale,
each outstanding option held by the Chief Executive Officer and the other
executive officers under the Company's 1994 Stock Plan (the predecessor equity
incentive program to the 1996 Plan) or the 1996 Plan will automatically
accelerate in full, except to the extent such options are to be assumed by the
successor corporation. In addition, the Compensation Committee as Plan
Administrator of the 1996 Plan will have the authority to provide for the
accelerated vesting of the shares of Common Stock subject to outstanding options
held by the Chief Executive Officer or any other executive officer or any
unvested shares of Common Stock subject to direct issuances held by such
individual, in connection with the termination of the officer's employment
following: (i) a merger or asset sale in which these options are assumed or are
assigned or (ii) certain hostile changes in control of the Company.

Deferred Compensation Plan

     Effective January 1, 2000 QuadraMed adopted a deferred compensation plan
(the"DCP") the purpose of which is to provide specified benefits to, and help
retain, a select group of management and highly compensated employees and
directors who contribute materially to the continued growth, development and
future business success of QuadraMed. The DCP is unfunded for tax purposes and
for purposes of Title I of ERISA. A committee of the board of directors is
responsible, in its sole discretion, to select the employees and directors to
participate in the DCP.

     Under the DCP, a participant may elect to defer for each plan year a
minimum amount of $2,000 of his or her base annual salary and a minimum amount
of $2,000 of his or her annual bonus, and a maximum amount of 90% (less
applicable withholding) of his or her base annual salary, a maximum amount of
90% (less applicable withholding) of his or her annual bonus, and 100% of his or
her director's fees. QuadraMed may, in its sole discretion, credit any amount it
desires to any participant's company contribution account. QuadraMed is required
to contribute a matching amount equal to 50% of a participant's annual deferral
amount, up to 2% of such participant's total annual compensation for each plan
year, to the participant's company contribution account. The amount contributed
by a participant is 100% vested at all times. The amount contributed by
QuadraMed is vested in relation to each participant's years of service after
January 1, 2000 as follows: (a) 0% if less than 1 year; (b) 25% for 1 year; (c)
50% for 2 years; (d) 75% for 3 years; and (e) 100% for 4 years or more. In the
event of a change in control or involuntary termination of employment, other
than a termination of employment for cause, a participant's company contribution
account immediately becomes 100% vested.

Stock Exchange Deferred Compensation Plan

     Effective January 3, 2000, QuadraMed adopted a Stock Exchange Deferred
Compensation Plan (the "SEDCP") the purpose of which is to provide specified
benefits to, and help retain, a select group of management and highly
compensated employees who contribute materially to the continued growth,
development and future business success of QuadraMed. The SEDCP is unfunded for
tax purposes and for purposes of Title I of ERISA. A committee of the board of
directors is responsible, in its sole discretion, to select the employees to
participate in the SEDCP.


     Under the SEDCP, QuadraMed is required to credit an amount to a
participant's account under the SEDCP as of the date specified in the
participant's Exchange Agreement. One-half of the amount so credited must be
credited to the participant's company stock account and the other half must be
credited to the participant's other investments account. A participant is vested
in his or her SEDCP account in relation to each participant's years of service
after January 3, 2000 as follows: (a) 0% if less than 3 years and (b) 100% if 3
years or more. In the event of a change in control, a participant's death,
disability, retirement or involuntary termination of employment, other than a
termination of employment for cause, a participant's SEDCP account immediately
becomes 100% vested.


     On January 3, 2000, James Durham entered into an Exchange Agreement with
QuadraMed pursuant to which Mr. Durham agreed that the stock options previously
granted to him in 1998 to acquire 300,000 shares of stock in QuadraMed would be
cancelled and in consideration for such cancellation, Mr. Durham would receive
an amount equal to $2,416,000 which would be credited to his SEDCP account in
accordance with the SEDCP. As of March 31, 2000, Mr. Durham's years of service
for purposes of vesting in his SEDCP account, which is based on years of
service after January 3, 2000, were three months.

     On January 3, 2000, John Cracchiolo entered into an Exchange Agreement with
QuadraMed pursuant to which Mr. Cracchiolo agreed that the stock options
previously granted to him in 1998 to acquire 150,000 shares of stock in
QuadraMed would be cancelled and in consideration for such cancellation, Mr.
Cracchiolo would receive an amount equal to $1,208,000 which would be credited
to his SEDCP account in accordance with the SEDCP. As of March 31, 2000, Mr.
Cracchiolo's years of service for purposes of vesting in his SEDCP account,
which is based on years of service after January 3, 2000, were three months.

Supplemental Executive Retirement Plan

     Effective January 1, 2000, QuadraMed adopted a Supplemental Executive
Retirement Plan (the "SERP") the purpose of which is to provide specified
benefits to, and help retain, a select group of management and highly
compensated employees who contribute materially to the continued growth,
development and future business success of QuadraMed. The SERP is unfunded for
tax purposes and for purposes of Title I of ERISA. A committee of the board of
directors is responsible, in its sole discretion, to select the employees to
participate in the SERP.

     Under the SERP, participants receive a 20-year installment benefit, payable
monthly and commencing at age sixty (60), equal to the product of 0.05
multiplied by such participant's highest annual compensation multiplied by his
or her years of service (not to exceed 13) multiplied by 1/12. A participant is
vested in his or her SERP benefit in relation to such participant's years of
participation in the plan on the date of termination of employment, as follows:
(a) 0% if less than 7 years and (b) 100% if 7 years or more. In the event of a
change in control, a participant's death, disability, retirement or involuntary
termination of employment, other than a termination of employment for cause, a
participant becomes immediately vested in his or her SERP benefit. In the event
of an involuntary termination, other than for cause, a participant is entitled
to a lump sum amount, rather than the installment payments described above,
equal to the actuarial equivalent of a 20-year monthly installment payment equal
to the product of 0.65 multiplied by the participant's highest annual
compensation multiplied by 1/12.

     The following table shows the estimated annual payments payable at normal
retirement to a SERP participant. The benefits shown in the table are not
subject to offset for Social Security or other benefits.

                               Pension Plan Table

                        Annual Benefits Upon Retirement
                        With Years of Service Indicated

<TABLE>
<CAPTION>
Highest Annual
Compensation                  5 Years             10 Years            15 Years
--------------                -------             --------            --------
<S>                           <C>                 <C>                 <C>
$500,000                      $125,000            $250,000            $325,000
$600,000                       150,000             300,000             390,000
$700,000                       175,000             350,000             455,000
$800,000                       200,000             400,000             520,000
$900,000                       225,000             450,000             585,000
</TABLE>

     For purposes of the SERP, "highest annual compensation" means a
participant's highest annual compensation, including salary and bonuses, during
the participant's last ten years of employment. The "salary" and "bonuses" used
to determine a participant's "highest annual compensation" are the same as the
salary and bonuses disclosed in the "Salary" and "Bonuses" columns of the
Summary Compensation Table.

     As of March 31, 2000, the "years of service" for Mr. Durham and Mr.
Cracchiolo were approximately 6.5 years and 5 years, respectively. For purposes
of vesting under the SERP, as of March 31, 2000 the "period of plan
participation" for both Mr. Durham and Mr. Cracchiolo was three months. No
other officers of the Company were participants in the SERP as of March 31,
2000.

Grantor Trust Agreement

        Effective January 1, 2000, QuadraMed entered into a Grantor Trust
Agreement with Wachovia Bank, N.A. pursuant to which QuadraMed agreed to make
contributions to a trust established pursuant to the agreement to satisfy
QuadraMed's obligations under the DCP, the SEDCP and the SERP. Under the terms
of the agreement, upon a threatened change in control the Company is required to
make contributions to the trust in an amount equal to not less than 100%, but
not more than 120%, of the amount necessary to pay the participants in such
plans the benefits they would be entitled to under the terms of such plans on
the date the threatened change in control occurs. In the event a change in
control does not occur within six months of the threatened change in control,
the Company has the right to recover such funds. Upon a change in control, the
Company is obligated to make an irrevocable contribution to the trust in an
amount equal to not less than 100%, but not more than 120%, of the amount
necessary to pay the participants in such plans the benefits they would be
entitled to under the terms of such plans on the date the change in control
occurs. The Company is also obligated to fund a $125,000 expense reserve for the
trustee upon a threatened change in control or a change in control. A
"threatened change in control" is defined to include any pending offer for the
Company's outstanding shares of common stock, any pending offer to acquire the
Company by merger, or any pending action or plan to effect a change in control.
A "change in control" is defined to include the merger of the Company into
another corporation if the Company is not the surviving corporation or if after
such transaction any person or group owns more than 50% of the outstanding
shares of common stock or assets of the Company, the sale or transfer to any
person or group in a single transaction or a series of related transactions of
more than 35% of the outstanding shares of common stock of the Company, the
acquisition by any person or group of substantially all of the assets of the
Company, or any other transaction the Board of Directors determines affects
control of the Company and constitutes a change in control.

          COMPENSATION COMMITTEE INTERLOCKS AND INSIDER PARTICIPATION

     The Company's Compensation Committee during the 1999 fiscal year consisted
of Mr. Roskovensky (Chairperson) and Mr. Greene. No member of such Committee
was at any time during the 1999 fiscal year or at any other time an officer or
employee of the Company. No executive officer of the Company served on the
compensation committee or another entity or any other committee of the
board of directors of another entity performing similar functions during the
Company's last fiscal year.


                                       11
<PAGE>   12
ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

     The following table sets forth certain information regarding the beneficial
ownership of the Company's Common Stock as of March 31, 2000 by (i) each person
(or group of affiliated persons) known by the Company to be the beneficial owner
of more than five percent of the outstanding shares of the Company's Common
Stock, (ii) each director of the Company, (iii) each Named Executive Officer of
the Company and (iv) all executive officers and directors of the Company as a
group.

<TABLE>
<CAPTION>
                                                                 SHARES OF
                                                                COMMON STOCK
                                                           BENEFICIALLY OWNED(1)
                                                           ----------------------
                 NAME OF BENEFICIAL OWNERS                   NUMBER      PERCENT
                 -------------------------                 ----------    --------
<S>                                                        <C>           <C>
Pilgrim Baxter & Associates, Ltd(2)......................  1,860,700        7.3%
  825 Duportail Road
  Wayne, PA 19087
AXA Financial, Inc.(3)...................................  1,408,488        5.5%
  1290 Avenue of the Americas
  New York, NY 10104
Nitin T. Mehta(4)........................................  1,326,362        5.2%
  58 Greenoaks Drive
  Atherton, CA 94027
Joe D. Whisenhunt, Sr.(5)................................  1,255,190        4.9%
  Harmony Meadows Ranch
  Route 2, Box 150
  Bee Branch, AR 72013
James D. Durham(6).......................................  1,330,469        5.2%
John V. Cracchiolo(7)....................................    480,000        1.9%
Keith M. Roberts(8)......................................    183,980          *
Nancy Nelson(9)..........................................    174,510          *
Patrick Ahearn(10).......................................    121,084          *
Michael Wilstead(11).....................................    100,000          *
Albert L. Greene(12).....................................     18,000          *
Scott Gross(13)..........................................     12,000          *
Michael J. King(14)......................................    159,322          *
Joan P. Neuscheler(15)...................................    145,493          *
E.A. Roskovensky(16).....................................     12,900          *
Cornelius T. Ryan(17)....................................     28,000          *
All executive officers and directors as a group (15
  persons)(18)...........................................  3,053,727         12%
</TABLE>

---------------
  *  Less than one percent.

 (1) Percentage ownership is based on approximately 25,473,688 shares of Common
     Stock outstanding on March 31, 2000. Beneficial ownership is determined in
     accordance with the rules of the Securities and Exchange Commission and
     generally includes voting or investment power with respect to securities.
     Shares of Common Stock subject to options, warrants and convertible notes
     currently exercisable or convertible, or exercisable or convertible within
     60 days, are deemed outstanding for computing the percentage of the person
     holding such options, but are not deemed outstanding for computing the
     percentage of any other person. Except as indicated by footnote, and
     subject to community property laws where applicable, the persons named in
     the table have sole voting and investment power with respect to all shares
     of Common Stock shown as beneficially owned by them.

                                        12


<PAGE>   13
 (2) Represents shares beneficially owned by Pilgrim Baxter & Associates, Ltd.
     ("Pilgrim Baxter") based on the information contained in Amendment No 2 to
     Schedule 13G filed on January 19, 1999. Pilgrim Baxter is an investment
     adviser registered under the Investment Advisers Act of 1940.

 (3) Represents shares beneficially owned by AXA Financial, Inc., formerly The
     Equitable Companies Incorporated ("AXA") based on information in a Schedule
     13G filed on February 14, 2000. All shares of the Common Stock reported as
     beneficially owned by AXA were directly beneficially owned by subsidiaries
     of AXA.

 (4) Represents shares beneficially owned by Nitin T. Mehta based on information
     contained in a Schedule 13G filed on June 15, 1998.

 (5) Represents shares beneficially owned by Joe D. Whisenhunt, Sr. based on
     information contained in a Schedule 13D filed on October 15, 1998. Share
     ownership shown is less than 5% of the outstanding shares of the Company's
     Common Stock. Details on share ownership are provided for informational
     purposes only.

 (6) Includes 23,295 shares of Common Stock owned by Trigon Resources
     Corporation ("Trigon"), a corporation owned by Mr. Durham and his two
     children and 134,574 shares of Common Stock issuable upon exercise of a
     warrant held by Trigon. Also includes 705,000 shares issuable upon exercise
     of options, 434,791 of which are exercisable within 60 days of March 31,
     2000 and 112,000 shares subject to a stock bonus award, which shares will
     be issued in October 2003, or earlier, in the event certain performance
     milestones are attained. Mr. Durham's address is 22 Pelican Way, San
     Rafael, California 94901.

 (7) Includes 420,000 shares issuable upon exercise of options, 265,416 of which
     are exercisable within 60 days of March 31, 2000 and 60,000 shares subject
     to a stock bonus award, which shares will be issued in October 2003, or
     earlier, in the event certain performance milestones are attained.

 (8) Includes 153,980 shares issuable upon exercise of options, 83,235 of which
     are exercisable within 60 days of March 31, 2000 and 30,000 shares subject
     to a stock bonus award, which shares will be issued in October 2003, or
     earlier, in the event certain performance milestones are attained.

 (9) Includes 174,510 shares of Common Stock issuable upon exercise of options,
     78,677 of which are exercisable within 60 days of March 31, 2000.

(10) Includes 121,084 Shares of Common Stock issuable upon exercise of options,
     40,667 of which are exercisable within 60 days of March 31, 2000.

(11) Includes 100,000 shares of Common Stock issuable upon exercise of options,
     18,958 of which are exercisable within 60 days of March 31, 2000.

(12) Includes 18,000 shares issuable upon exercise of options, 17,000 of which
     are exercisable within 60 days of March 31, 2000.

(13) Includes 12,000 shares of Common Stock issuable upon exercise of options,
     2,000 of which are exercisable within 60 days of March 31, 2000.

(14) Includes 159,322 shares issuable upon exercise of options, 159,322 of which
     are exercisable within 60 days of March 31, 2000.

(15) Includes 122,005 shares of Common Stock issuable upon exercise of certain
     warrants issued to Tullis-Dickerson Capital Focus, L.P. Also includes
     22,000 shares issuable upon exercise of options held by Ms. Neuscheler,
     21,000 of which are exercisable within 60 days of March 31, 2000. Ms.
     Neuscheler, a director of the Company, is a general partner of
     Tullis-Dickerson Partners, which is the general partner of Tullis-Dickerson
     Capital Focus, L.P. Ms. Neuscheler disclaims beneficial ownership in the
     shares held by Tullis-Dickerson Capital Focus, L.P., except to the extent
     of her pecuniary interest arising from her general partnership interest in
     Tullis-Dickerson Partners. Also includes 744 shares held in trust for the
     benefit of Susannah Dickerson and 744 shares held in trust for the benefit
     of Caroline Dickerson. Ms. Neuscheler disclaims beneficial ownership in
     such shares.

(16) Includes 10,000 shares of Common Stock issuable upon exercise of options,
     none of which are exercisable within 60 days of March 31, 2000.

(17) Includes 28,000 shares of Common Stock issuable upon exercise of options,
     18,000 of which are exercisable within 60 days of March 31, 2000.

(18) Includes 23,295 shares of Common Stock owned by Trigon Resources
     Corporation ("Trigon"), a corporation owned by Mr. Durham and his two
     children and 134,574 shares of Common Stock issuable upon exercise of a
     warrant held by Trigon. Includes 2,211,865 shares issuable upon exercise
     of options, 1,154,067 of which shares are exercisable within 60 days of
     March 31, 2000 and 202,000 shares subject to a stock bonus award, which
     shares will be issued in October 2003, or earlier, in the event certain
     performance milestones are attained.

                                       13

<PAGE>   14
ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS.

        In addition to the indemnification provisions contained in the Company's
Restated Certificate of Incorporation and Bylaws, the Company has entered into
separate indemnification agreements with each of its directors and officers.
These agreements require the Company, among other things to indemnify such
director or officer against expenses (including attorneys' fees), judgments,
fines and settlements (collectively, "Liabilities") paid by such individual in
connection with any action, suite or proceeding arising out of such individual's
status or service as a director or officer of the Company (other than
Liabilities arising from willful misconduct or conduct that is knowingly
fraudulent or deliberately dishonest) and to advance expenses incurred by such
individual in connection with any proceeding against such individual with
respect to which such individual may be entitled to indemnification by the
Company.

        Michael King, a director of the Company, is the Chief Executive Officer
of Healthscribe, Inc., a provider of transcription services. During 1999,
QuadraMed paid a total of $717,278 to Healthscribe, Inc. for transcription
services.

                                PART IV

ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K.

        Item 14(c) is hereby amended by adding the following exhibits:

10.60   QuadraMed Corporation Deferred Compensation Plan, effective January 1,
        2000

10.61   QuadraMed Corporation Stock Exchange Deferred Compensation Plan,
        effective January 3, 2000

10.62   Exchange Agreement dated January 3, 2000 between QuadraMed Corporation
        and Jim Durham

10.63   Exchange Agreement dated January 3, 2000 between QuadraMed Corporation
        and John Cracchiolo

10.64   QuadraMed Corporation Supplemental Executive Retirement Plan, effective
        January 1, 2000

10.65   Grantor Trust Agreement dated January 1, 2000 between QuadraMed
        Corporation and Wachovia Bank, N.A.


                                       14
<PAGE>   15
                                   SIGNATURES

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

                                       QUADRAMED CORPORATION

Date: MAY 26, 2000
                                       By:  /s/ JOHN V. CRACCHIOLO
                                            ------------------------------------
                                             John V. Cracchiolo
                                             President, Chief Financial
                                             Officer and Secretary

        Pursuant to the requirements of the Securities Exchange Act of 1934,
this report has been signed by the following persons in the capacities and on
the dates indicated:


<TABLE>
<CAPTION>
             SIGNATURE                                  TITLE                            DATE
             ---------                                  -----                            ----
<S>                                    <C>                                             <C>
/s/ JAMES D. DURHAM                    Chairman of the Board                           May 26, 2000
----------------------------------     and Chief Executive Officer
          James D Durham               (Principal Executive Officer)

/s/ JOHN V. CRACCHIOLO                 President,                                      May 26, 2000
----------------------------------     Chief Financial Officer and
          John V. Cracchiolo           Secretary (Principal Financial and
                                       Accounting Officer)

/s/ ALBERT L. GREENE*                  Director                                        May 26, 2000
-----------------------------------
         Albert L. Greene

/s/ SCOTT GROSS*                       Director                                        May 26, 2000
-----------------------------------
         Scott Gross

/s/ MICHAEL J. KING*                   Director                                        May 26, 2000
-----------------------------------
         Michael J. King

/s/ E. A. ROSKOVENSKY*                 Director                                        May 26, 2000
-----------------------------------
         E. A. Roskovensky

/s/ CORNELIUS T. RYAN*                 Director                                        May 26, 2000
-----------------------------------
         Cornelius T. Ryan

* By /s/ JOHN V. CRACCHIOLO
     ------------------------------
         John V. Cracchiolo,
         Attorney-In-Fact
</TABLE>


                                       15
<PAGE>   16
                                  EXHIBIT INDEX

10.60   QuadraMed Corporation Deferred Compensation Plan, effective January 1,
        2000

10.61   QuadraMed Corporation Stock Exchange Deferred Compensation Plan,
        effective January 3, 2000

10.62   Exchange Agreement dated January 3, 2000 between QuadraMed Corporation
        and Jim Durham

10.63   Exchange Agreement dated January 3, 2000 between QuadraMed Corporation
        and John Cracchiolo

10.64   QuadraMed Corporation Supplemental Executive Retirement Plan effective
        January 1, 2000

10.65   Grantor Trust Agreement dated January 1, 2000 between QuadraMed
        Corporation and Wachovia Bank, N.A.

<PAGE>   17
                              QUADRAMED CORPORATION

                         1999 FORM 10-K/A ANNUAL REPORT

                                 AMENDMENT NO. 2

                                TABLE OF CONTENTS
<TABLE>
<CAPTION>
                                                                             PAGE
<S>                                                                          <C>
PART III....................................................................   2

ITEM 10.   DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT...............   2

ITEM 11.   EXECUTIVE COMPENSATION...........................................   7

ITEM 12.   SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT...  12

ITEM 13.   CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS...................  14

PART IV.....................................................................  14

ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K...  14

SIGNATURES..................................................................  15
</TABLE>