| 1. Round | 07/08/1999 | KVC Westerlo | - | KRC Genk | 6:6 |  |
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| 2. Round | 14/08/1999 | KAA Gent | - | KRC Genk | 0:2 | ||||
| 3. Round | 21/08/1999 | Verbroedering Geel | - | KRC Genk | 1:1 | ||||
| 4. Round | 29/08/1999 | KRC Genk | - | Standard Liège | 4:0 | ||||
| 5. Round | 11/09/1999 | RSC Charleroi | - | KRC Genk | 2:1 | |
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| 6. Round | 18/09/1999 | KRC Genk | - | Excelsior Mouscron | 2:2 | |
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| 7. Round | 25/09/1999 | KSK Beveren | - | KRC Genk | 1:4 | |
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| 8. Round | 03/10/1999 | KRC Genk | - | Lierse SK (old) | 2:2 | |
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| 9. Round | 13/10/1999 | Lommelse SK | - | KRC Genk | 0:1 | ||||
| 10. Round | 24/10/1999 | KRC Genk | - | Club Brugge KV | 1:0 | |
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| 12. Round | 06/11/1999 | KRC Genk | - | Sporting Lokeren | 1:1 | ||||
| 13. Round | 10/11/1999 | KRC Genk | - | Germinal Beerschot | 4:0 | |
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| 14. Round | 20/11/1999 | KRC Genk | - | K.S.C. Eendracht Aalst | 2:1 | ||||
| 15. Round | 28/11/1999 | RSC Anderlecht | - | KRC Genk | 1:3 | |
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| 17. Round | 11/12/1999 | KV Mechelen | - | KRC Genk | 2:0 |  |
Croatia