| 6. Round | 29/08/2009 | VfL Osnabrück | - | FC Carl Zeiss Jena | 2:0 | ||||
| 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 |  |
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| 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 | ||||
| 12. Round | 03/10/2009 | Kickers Offenbach | - | FC Carl Zeiss Jena | 4:0 | ||||
| 15. Round | 31/10/2009 | Jahn Regensburg | - | FC Carl Zeiss Jena | 1:1 | ||||
| 16. Round | 07/11/2009 | FC Carl Zeiss Jena | - | Dynamo Dresden | 0:4 | ||||
| 21. Round | 23/01/2010 | FC Carl Zeiss Jena | - | SV Sandhausen | 0:1 | ||||
| 23. Round | 06/02/2010 | FC Carl Zeiss Jena | - | Erzgebirge Aue | 1:0 | ||||
| 25. Round | 21/02/2010 | FC Carl Zeiss Jena | - | VfL Osnabrück | 1:1 | ||||
| 28. Round | 27/04/2010 | Wacker Burghausen | - | FC Carl Zeiss Jena | 2:3 | ||||
| 37. Round | 30/04/2010 | Wuppertaler SV | - | FC Carl Zeiss Jena | 1:1 |  |
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| 38. Round | 08/05/2010 | FC Carl Zeiss Jena | - | VfB Stuttgart II | 1:2 | |
Germany