| 1. Round | 07/08/1999 | RSC Charleroi | - | KRC Harelbeke | 2:1 | ||||
| 2. Round | 15/08/1999 | KRC Harelbeke | - | Excelsior Mouscron | 1:1 | ||||
| 3. Round | 21/08/1999 | KSK Beveren | - | KRC Harelbeke | 2:2 | ||||
| 4. Round | 29/08/1999 | KRC Harelbeke | - | Lierse SK | 0:3 | ||||
| 5. Round | 11/09/1999 | Lommelse SK | - | KRC Harelbeke | 0:2 |  |
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| 6. Round | 19/09/1999 | KRC Harelbeke | - | Club Brugge KV | 1:1 | ||||
| 7. Round | 25/09/1999 | Sint-Truidense VV | - | KRC Harelbeke | 2:0 | ||||
| 10. Round | 24/10/1999 | KRC Harelbeke | - | K.S.C. Eendracht Aalst | 1:1 | ||||
| 25. Round | 04/03/2000 | Sporting Lokeren | - | KRC Harelbeke | 2:0 | ||||
| 26. Round | 12/03/2000 | KRC Harelbeke | - | Germinal Beerschot | 1:0 | ||||
| 27. Round | 19/03/2000 | K.S.C. Eendracht Aalst | - | KRC Harelbeke | 3:0 | ||||
| 28. Round | 26/03/2000 | KRC Harelbeke | - | RSC Anderlecht | 2:2 | ||||
| 29. Round | 02/04/2000 | Verbroedering Geel | - | KRC Harelbeke | 3:2 | |
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| 30. Round | 09/04/2000 | KV Mechelen | - | KRC Harelbeke | 4:0 | ||||
| 31. Round | 16/04/2000 | KRC Harelbeke | - | KVC Westerlo | 3:1 | ||||
| 33. Round | 06/05/2000 | KRC Harelbeke | - | KRC Genk | 1:2 | ||||
| 34. Round | 11/05/2000 | Standard Liège | - | KRC Harelbeke | 1:3 |
Russia