| 2. Round | 03/08/2005 | FC Carl Zeiss Jena | - | Bayer Leverkusen II | 1:1 | ||||
| 3. Round | 06/08/2005 | Hertha BSC II | - | FC Carl Zeiss Jena | 1:3 | ||||
| 5. Round | 20/08/2005 | Chemnitzer FC | - | FC Carl Zeiss Jena | 1:3 | ||||
| 8. Round | 09/09/2005 | VfL Osnabrück | - | FC Carl Zeiss Jena | 2:2 |  |
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| 9. Round | 16/09/2005 | FC Carl Zeiss Jena | - | SG Wattenscheid 09 | 1:0 | ||||
| 10. Round | 21/09/2005 | Rot-Weiss Essen | - | FC Carl Zeiss Jena | 2:1 | ||||
| 11. Round | 24/09/2005 | FC Carl Zeiss Jena | - | 1. FC Köln II | 2:1 | ||||
| 12. Round | 01/10/2005 | FC St. Pauli | - | FC Carl Zeiss Jena | 1:2 | ||||
| 13. Round | 15/10/2005 | FC Carl Zeiss Jena | - | Hamburger SV II | 2:1 | ||||
| 14. Round | 22/10/2005 | Werder Bremen II | - | FC Carl Zeiss Jena | 0:2 | ||||
| 15. Round | 29/10/2005 | FC Carl Zeiss Jena | - | Rot-Weiß Erfurt | 2:0 | ||||
| 16. Round | 05/11/2005 | Kickers Emden | - | FC Carl Zeiss Jena | 1:2 | ||||
| 18. Round | 19/11/2005 | Fortuna Düsseldorf | - | FC Carl Zeiss Jena | 3:1 | ||||
| 36. Round | 13/05/2006 | VfB Lübeck | - | FC Carl Zeiss Jena | 0:0 |
Germany