| 1. Round | 13/08/1999 | Energie Cottbus | - | Fortuna Köln | 2:0 | ||||
| 3. Round | 29/08/1999 | 1. FC Nürnberg | - | Fortuna Köln | 2:1 | ||||
| 4. Round | 12/09/1999 | Fortuna Köln | - | Chemnitzer FC | 1:0 | ||||
| 5. Round | 19/09/1999 | Hannover 96 | - | Fortuna Köln | 3:1 |  |
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| 6. Round | 25/09/1999 | Fortuna Köln | - | Karlsruher SC | 2:3 |  |
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| 7. Round | 01/10/1999 | Alemannia Aachen | - | Fortuna Köln | 1:1 | ||||
| 8. Round | 15/10/1999 | Fortuna Köln | - | FC St. Pauli | 2:0 | ||||
| 9. Round | 25/10/1999 | 1. FC Köln | - | Fortuna Köln | 3:0 | ||||
| 10. Round | 31/10/1999 | Fortuna Köln | - | Rot-Weiß Oberhausen | 0:0 | ||||
| 11. Round | 07/11/1999 | SpVgg Greuther Fürth | - | Fortuna Köln | 0:0 | ||||
| 12. Round | 19/11/1999 | Fortuna Köln | - | Stuttgarter Kickers | 1:1 | ||||
| 13. Round | 27/11/1999 | VfL Bochum | - | Fortuna Köln | 3:0 | ||||
| 14. Round | 05/12/1999 | Fortuna Köln | - | TeBe Berlin | 0:0 | ||||
| 15. Round | 12/12/1999 | Bor. Mönchengladbach | - | Fortuna Köln | 0:0 | ||||
| 16. Round | 15/12/1999 | Fortuna Köln | - | Waldhof Mannheim | 1:5 | ||||
| 17. Round | 19/12/1999 | Kickers Offenbach | - | Fortuna Köln | 4:3 |
Austria