| 1. Round | 06/08/2006 | FC Carl Zeiss Jena II | - | VfB Pößneck | 1:0 | ||||
| 2. Round | 12/08/2006 | VfB Auerbach | - | FC Carl Zeiss Jena II | 0:0 | ||||
| 4. Round | 26/08/2006 | Chemnitzer FC | - | FC Carl Zeiss Jena II | 2:1 | ||||
| 5. Round | 09/09/2006 | FSV Zwickau | - | FC Carl Zeiss Jena II | 1:0 | ||||
| 6. Round | 24/09/2006 | Sachsen Leipzig | - | FC Carl Zeiss Jena II | 2:1 |  |
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| 7. Round | 30/09/2006 | FC Carl Zeiss Jena II | - | FSV Budissa Bautzen | 0:3 | ||||
| 8. Round | 14/10/2006 | Hallescher FC | - | FC Carl Zeiss Jena II | 2:0 | ||||
| 9. Round | 21/10/2006 | FC Carl Zeiss Jena II | - | SV Dessau 05 | 1:0 | ||||
| 11. Round | 04/11/2006 | FC Carl Zeiss Jena II | - | Germania Halberstadt | 3:0 | ||||
| 12. Round | 11/11/2006 | FC Eilenburg | - | FC Carl Zeiss Jena II | 1:0 | ||||
| 15. Round | 03/12/2006 | ZFC Meuselwitz | - | FC Carl Zeiss Jena II | 2:0 | ||||
| 16. Round | 10/12/2006 | VfB Pößneck | - | FC Carl Zeiss Jena II | 0:0 |
Germany