<PAGE>
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
 
                       SECURITIES AND EXCHANGE COMMISSION
                              WASHINGTON, DC 20549
 
                            ------------------------
 
                          FORM 10-K/A AMENDMENT NO. 1
 
/X/           ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                        SECURITIES EXCHANGE ACT OF 1934
 
                  FOR THE FISCAL YEAR ENDED SEPTEMBER 30, 1998
 
                                       OR
 
/ /         TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
               SECURITIES EXCHANGE ACT OF 1934 (NO FEE REQUIRED)
 
     FOR THE TRANSITION PERIOD FROM                   TO
 
                        COMMISSION FILE NUMBER 0-27502.
 
                            ------------------------
 
                       HEALTH SYSTEMS DESIGN CORPORATION
             (Exact name of registrant as specified in its charter)
 
<TABLE>
<S>                           <C>
          DELAWARE                 94-3235734
(State or other Jurisdiction    (I.R.S. Employer
             of                  Identification
      Incorporation or               Number)
       Organization)
</TABLE>
 
                    1330 BROADWAY, OAKLAND, CALIFORNIA 94612
              (Address of principal executive offices) (Zip code)
 
                                 (510) 763-2629
              (Registrant's telephone number, including area code)
 
    Securities registered pursuant to Section 12(b) of the Act:
 
<TABLE>
<CAPTION>
  Title of each        Name of each exchange on which
      Class                      registered
<S>                <C>
      NONE                          NONE
</TABLE>
 
    Securities registered pursuant to Section 12(g) of the Act:
 
                                  COMMON STOCK
                                (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 reports), 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 registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K.  / /
 
    As of November 30, 1998, 6,673,307 shares of the registrant's common stock
were outstanding. The aggregate market value of the common stock held by
non-affiliates of the registrant on that date was approximately $13,566,600.
 
    Portions of the definitive proxy statement for the Company's annual meeting
of stockholders, to be held on March 23, 1999, are incorporated by reference
into Part III of this Form 10-K.
 
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
<PAGE>
                                    PART IV
 
   
    Item 14 of the Annual Report filed pursuant to Section 13 or 15(d) of the
Securities Exchange Act of 1934, as amended, for the fiscal year ended September
30, 1998 is hereby amended in full as follows:
    
 
    ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON FORM 8-K
 
    (a) See Index to Consolidated Financial Statements at Item 8. of this
       report.
 
   
<TABLE>
<CAPTION>
 EXHIBIT     DESCRIPTION
-----------  ---------------------------------------------------------------------------------------------------------
<C>          <S>
       3.1   Certificate of Incorporation of the Registrant, as amended (Incorporated by reference from Exhibit 3.1 to
             Registration Statement No. 333-0094)
 
       3.2   By-laws of the Registrant (Incorporated by reference from Exhibit 3.2 to Registration Statement No.
             333-0094)
 
       4.1   Specimen Common Stock Certificate (Incorporated by reference from Exhibit 4.1 to Registration Statement
             No. 333-0094)
 
      10.1   Office building lease, dated February 24, 1994, as amended, for the Registrant's principal executive
             offices (Incorporated by reference from Exhibit 10.1 to Registration Statement No. 333-0094)
 
     10.1.1  Office building lease, dated October 28, 1998, for the Registrant's principal executive offices
 
      10.2   1994 Equity Incentive Plan (Incorporated by reference from Exhibit 3.1 to Registration Statement No.
             333-0094)*
 
      10.3   1996 Omnibus Equity Incentive Plan (Incorporated by reference from Exhibit 10.3 to Registration Statement
             No. 333-0094)*
 
      10.4   Marketing Agreement dated January 31, 1994 between the Registrant and Shared Medical Systems Corporation
             (Incorporated by reference from Exhibit 10.4 to Registration Statement No. 333-0094)+
 
     10.4.1  Amendment to HSD/SMS Marketing Agreement, dated December 19, 1997 (Incorporated by reference from Exhibit
             10.4.1 to Registrant's Annual Report on Form 10-K for the fiscal year ended September 30, 1997)+
 
      10.6   Promissory Note, dated May 31, 1995, issued by the Registrant to SVB (Incorporated by reference from
             Exhibit 10.6 to Registration Statement No. 333-0094)
 
      10.7   Commercial Security Agreement, dated May 31, 1995, between the Registrant and SVB (Incorporated by
             reference from Exhibit 10.7 to Registration Statement No. 333-0094)
 
      10.12  Business Loan Agreement, effective August 22, 1995, between the Registrant and SVB (Incorporated by
             reference from Exhibit 10.12 to Registration Statement No. 333-0094)
 
      10.14  Commercial Security Agreement, dated August 15, 1995, between the Registrant and SVB (Incorporated by
             reference from Exhibit 10.14 to Registration Statement No. 333-0094)
 
      10.15  Loan Modification Agreement, dated January 4, 1996, to SVB Business Loan Agreement (Incorporated by
             reference from Exhibit 10.15 to Registration Statement No. 333-0094)
 
      10.16  Promissory Note, dated May 6, 1994, issued by the Registrant to Wells Fargo Bank, National Association
             (Incorporated by reference from Exhibit 10.16 to Registration Statement No. 333-0094)
 
      10.17  Note and Warrant Purchase Agreement dated December 14, 1995 between the Registrant and the Purchasers
             listed on Exhibit A thereto (Incorporated by reference from Exhibit 10.17 to Registration Statement No.
             333-0094)
</TABLE>
    
 
                                       41
<PAGE>
   
<TABLE>
<CAPTION>
 EXHIBIT     DESCRIPTION
-----------  ---------------------------------------------------------------------------------------------------------
<C>          <S>
      10.23  Advisory Agreement dated July 18, 1995 between the Registrant and Mackowski & Shepler (Incorporated by
             reference from Exhibit 10.23 to Registration Statement No. 333-0094)
 
      10.24  Form of Indemnification Agreement between the Registrant and its directors and executive officers
             (Incorporated by reference from Exhibit 10.24 to Registration Statement No. 333-0094)
 
      10.25  Registrant's 401(k) Plan, as amended (Incorporated by reference from Exhibit 10.25 to Registration
             Statement No. 333-0094)
 
      10.26  License Agreement, dated March 25, 1996 between the Registrant and Blue Cross/Blue Shield of Florida
             (Incorporated by reference from Exhibit 10.26 to Registration Statement No. 333-0094)+
 
      10.27  Master Agreement, dated January 24, 1997 between Registrant and Blue Cross/Blue Shield of North Carolina
             (Incorporated by reference from Exhibit 10.27 to Registrant's Quarterly Report on Form 10-Q for the
             quarter ended March 31, 1997)+
 
      10.28  License Agreement, dated October 20, 1997 between the Registrant and Kaiser Permanente (Incorporated by
             reference from Exhibit 10.27 to Registrant's Quarterly Report on Form 10-Q for the quarter ended December
             31, 1997)+
 
      10.29  Management Contract, dated July 23, 1998 between the Registrant and Russell J. Harrison*
 
      11.1   Computation of net loss per share
 
      21.1   List of Subsidiaries
 
      23.1   Consent of Arthur Andersen LLP
 
      27     Financial Data Schedule
</TABLE>
    
 
------------------------
 
+   Confidential treatment has been granted with respect to portions of this
    exhibit.
 
*   Indicates, as required by Item 14(a)(3), a management contract or
    compensation plan required to be filed as an exhibit to this Form 10-K.
 
    (b) Reports on Form 8-K
 
   
    No reports on Form 8-K were filed during the fourth quarter of fiscal 1998.
    
 
    (c) See attached Exhibit Index.
 
    (d) The following financial statement schedules are filed as part of this
       report on page 42.
 
SCHEDULE II--VALUATION OF QUALIFYING ACCOUNTS
 
    All other schedules required by Form 10-K Annual Report have been omitted
because they were not applicable, were included in the notes to the consolidated
financial statements, or were otherwise not required under the instructions
contained in Regulation S-X.
 
                                       42
<PAGE>
                                   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.
 
   
<TABLE>
<C>                             <S>        <C>
                                HEALTH SYSTEMS DESIGN CORPORATION
 
                                By:                /s/ RUSSELL J. HARRISON
                                           ----------------------------------------
                                                     Russell J. Harrison,
                                            PRESIDENT AND CHIEF EXECUTIVE OFFICER
 
                                Date:         December 29, 1998
</TABLE>
    
 
                                       43