| 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 |  |
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| 3. Round | 20/08/2006 | FC Carl Zeiss Jena II | - | VFC Plauen | 1:1 | |
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| 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 | |
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| 6. Round | 24/09/2006 | Sachsen Leipzig | - | FC Carl Zeiss Jena II | 2:1 |  |
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| 8. Round | 14/10/2006 | Hallescher FC | - | FC Carl Zeiss Jena II | 2:0 | |
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| 9. Round | 21/10/2006 | FC Carl Zeiss Jena II | - | SV Dessau 05 | 1:0 |  |
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| 11. Round | 04/11/2006 | FC Carl Zeiss Jena II | - | Germania Halberstadt | 3:0 | |
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| 12. Round | 11/11/2006 | FC Eilenburg | - | FC Carl Zeiss Jena II | 1:0 | ||||
| 13. Round | 18/11/2006 | Rot-Weiß Erfurt II | - | FC Carl Zeiss Jena II | 1:3 | ||||
| 14. Round | 25/11/2006 | FC Carl Zeiss Jena II | - | Energie Cottbus II | 0:0 | ||||
| 15. Round | 03/12/2006 | ZFC Meuselwitz | - | FC Carl Zeiss Jena II | 2:0 | |
Germany