| 1. Round | 06/08/2006 | FC Carl Zeiss Jena II | - | VfB Pößneck | 1:0 | ||||
| 3. Round | 20/08/2006 | FC Carl Zeiss Jena II | - | VFC Plauen | 1:1 | ||||
| 5. Round | 09/09/2006 | FSV Zwickau | - | FC Carl Zeiss Jena II | 1:0 | ||||
| 8. Round | 14/10/2006 | Hallescher FC | - | FC Carl Zeiss Jena II | 2:0 | ||||
| 13. Round | 18/11/2006 | Rot-Weiß Erfurt II | - | FC Carl Zeiss Jena II | 1:3 | ||||
| 15. Round | 03/12/2006 | ZFC Meuselwitz | - | FC Carl Zeiss Jena II | 2:0 |  |
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| 16. Round | 10/12/2006 | VfB Pößneck | - | FC Carl Zeiss Jena II | 0:0 | |
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| 23. Round | 18/04/2007 | FC Carl Zeiss Jena II | - | Hallescher FC | 0:1 | ||||
| 24. Round | 22/04/2007 | SV Dessau 05 | - | FC Carl Zeiss Jena II | 0:1 | ||||
| 25. Round | 28/04/2007 | FC Carl Zeiss Jena II | - | FV Dresden-Nord | 1:1 | ||||
| 27. Round | 12/05/2007 | FC Carl Zeiss Jena II | - | FC Eilenburg | 0:3 |
Germany