| 16. Round | 08/12/2006 | 1. FC Kaiserslautern | - | FC Carl Zeiss Jena | 0:0 | ||||
| 17. Round | 15/12/2006 | FC Carl Zeiss Jena | - | FC Augsburg | 0:2 |  |
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| 21. Round | 11/02/2007 | FC Carl Zeiss Jena | - | Rot-Weiss Essen | 2:0 | ||||
| 22. Round | 18/02/2007 | SC Paderborn 07 | - | FC Carl Zeiss Jena | 0:1 | ||||
| 23. Round | 23/02/2007 | FC Carl Zeiss Jena | - | TSV 1860 München | 3:1 | ||||
| 25. Round | 11/03/2007 | FC Carl Zeiss Jena | - | Karlsruher SC | 1:3 | ||||
| 26. Round | 16/03/2007 | TuS Koblenz | - | FC Carl Zeiss Jena | 0:0 | |
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| 27. Round | 30/03/2007 | FC Carl Zeiss Jena | - | Hansa Rostock | 1:2 | ||||
| 29. Round | 16/04/2007 | FC Carl Zeiss Jena | - | Erzgebirge Aue | 2:1 | ||||
| 30. Round | 22/04/2007 | SC Freiburg | - | FC Carl Zeiss Jena | 1:3 | |
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| 31. Round | 27/04/2007 | FC Carl Zeiss Jena | - | MSV Duisburg | 3:3 | ||||
| 32. Round | 06/05/2007 | Wacker Burghausen | - | FC Carl Zeiss Jena | 1:1 | ||||
| 33. Round | 13/05/2007 | FC Carl Zeiss Jena | - | 1. FC Kaiserslautern | 1:1 | ||||
| 34. Round | 20/05/2007 | FC Augsburg | - | FC Carl Zeiss Jena | 1:2 | |
Germany