| 16. Round | 30/11/1998 | 1. FC Köln | - | Karlsruher SC | 4:1 | ||||
| 17. Round | 07/12/1998 | Arminia Bielefeld | - | 1. FC Köln | 0:0 | ||||
| 18. Round | 13/12/1998 | 1. FC Köln | - | FC Gütersloh | 1:1 | ||||
| 19. Round | 20/12/1998 | SpVgg Unterhaching | - | 1. FC Köln | 2:0 |  |
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| 20. Round | 26/02/1999 | 1. FC Köln | - | Hannover 96 | 0:2 | |
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| 21. Round | 07/03/1999 | SSV Ulm 1846 | - | 1. FC Köln | 2:2 | ||||
| 22. Round | 14/03/1999 | 1. FC Köln | - | 1. FSV Mainz 05 | 2:1 | ||||
| 23. Round | 22/03/1999 | FC St. Pauli | - | 1. FC Köln | 0:0 | ||||
| 24. Round | 04/04/1999 | 1. FC Köln | - | Energie Cottbus | 2:2 |  |
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| 25. Round | 09/04/1999 | Rot-Weiß Oberhausen | - | 1. FC Köln | 0:4 | |
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| 26. Round | 19/04/1999 | 1. FC Köln | - | Fortuna Köln | 0:3 | ||||
| 30. Round | 16/05/1999 | 1. FC Köln | - | TeBe Berlin | 1:0 | ||||
| 31. Round | 23/05/1999 | SpVgg Greuther Fürth | - | 1. FC Köln | 0:1 | ||||
| 32. Round | 28/05/1999 | 1. FC Köln | - | SG Wattenscheid 09 | 2:1 | ||||
| 33. Round | 13/06/1999 | Karlsruher SC | - | 1. FC Köln | 3:1 | |
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| 34. Round | 17/06/1999 | 1. FC Köln | - | Arminia Bielefeld | 3:5 | |
Germany