| 1. Round | 30/07/2005 | Rot-Weiß Erfurt | - | 1. FC Köln II | 4:3 | ||||
| 2. Round | 03/08/2005 | 1. FC Köln II | - | Kickers Emden | 0:3 | ||||
| 3. Round | 06/08/2005 | VfB Lübeck | - | 1. FC Köln II | 4:1 | ||||
| 5. Round | 23/08/2005 | Rot-Weiß Oberhausen | - | 1. FC Köln II | 2:2 | ||||
| 18. Round | 19/11/2005 | Hamburger SV II | - | 1. FC Köln II | 0:1 | ||||
| 28. Round | 18/03/2006 | 1. FC Köln II | - | Preußen Münster | 0:2 | ||||
| 29. Round | 25/03/2006 | Chemnitzer FC | - | 1. FC Köln II | 0:3 | ||||
| 26. Round | 29/03/2006 | 1. FC Köln II | - | Bayer Leverkusen II | 5:0 |  |
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| 30. Round | 01/04/2006 | 1. FC Köln II | - | FC Carl Zeiss Jena | 1:1 | ||||
| 31. Round | 08/04/2006 | Holstein Kiel | - | 1. FC Köln II | 5:1 | ||||
| 32. Round | 15/04/2006 | 1. FC Köln II | - | VfL Osnabrück | 0:0 |  |
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| 33. Round | 22/04/2006 | SG Wattenscheid 09 | - | 1. FC Köln II | 4:2 | ||||
| 38. Round | 27/05/2006 | Werder Bremen II | - | 1. FC Köln II | 2:2 |
Germany