| 1. Round | 25/07/2009 | FC Carl Zeiss Jena | - | SV Wehen Wiesbaden | 2:1 | ||||
| 2. Round | 29/07/2009 | SV Sandhausen | - | FC Carl Zeiss Jena | 2:2 | ||||
| 3. Round | 09/08/2009 | FC Carl Zeiss Jena | - | Bayern München II | 6:0 | ||||
| 4. Round | 15/08/2009 | Erzgebirge Aue | - | FC Carl Zeiss Jena | 0:0 | ||||
| 5. Round | 23/08/2009 | FC Carl Zeiss Jena | - | Rot-Weiß Erfurt | 0:3 | ||||
| 6. Round | 29/08/2009 | VfL Osnabrück | - | FC Carl Zeiss Jena | 2:0 |  |
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| 7. Round | 02/09/2009 | FC Carl Zeiss Jena | - | Borussia Dortmund II | 2:1 | ||||
| 8. Round | 05/09/2009 | Holstein Kiel | - | FC Carl Zeiss Jena | 0:1 | ||||
| 9. Round | 12/09/2009 | FC Carl Zeiss Jena | - | Wacker Burghausen | 0:0 | ||||
| 10. Round | 20/09/2009 | Eintracht Braunschweig | - | FC Carl Zeiss Jena | 2:1 | ||||
| 11. Round | 26/09/2009 | FC Carl Zeiss Jena | - | Werder Bremen II | 2:2 | ||||
| 26. Round | 17/03/2010 | Borussia Dortmund II | - | FC Carl Zeiss Jena | 0:3 | ||||
| 30. Round | 28/03/2010 | Werder Bremen II | - | FC Carl Zeiss Jena | 1:2 | ||||
| 31. Round | 31/03/2010 | FC Carl Zeiss Jena | - | Kickers Offenbach | 0:0 |
Germany