| 21. Round | 11/02/2007 | Wacker Burghausen | - | TuS Koblenz | 0:0 | ||||
| 23. Round | 25/02/2007 | Wacker Burghausen | - | SpVgg Greuther Fürth | 3:4 | ||||
| 24. Round | 04/03/2007 | Hansa Rostock | - | Wacker Burghausen | 0:0 | ||||
| 25. Round | 09/03/2007 | Wacker Burghausen | - | SC Freiburg | 2:2 | ||||
| 27. Round | 30/03/2007 | Wacker Burghausen | - | SpVgg Unterhaching | 4:1 |  |
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| 28. Round | 08/04/2007 | Wacker Burghausen | - | 1. FC Kaiserslautern | 0:0 | ||||
| 29. Round | 15/04/2007 | Kickers Offenbach | - | Wacker Burghausen | 2:1 | ||||
| 30. Round | 22/04/2007 | Wacker Burghausen | - | FC Augsburg | 0:2 |  |
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| 31. Round | 27/04/2007 | Eintracht Braunschweig | - | Wacker Burghausen | 3:1 | |
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| 32. Round | 06/05/2007 | Wacker Burghausen | - | FC Carl Zeiss Jena | 1:1 | ||||
| 33. Round | 13/05/2007 | Rot-Weiss Essen | - | Wacker Burghausen | 1:1 | ||||
| 34. Round | 20/05/2007 | Wacker Burghausen | - | SC Paderborn 07 | 5:1 | |
North Macedonia