| 1. Round | 26/07/2008 | Wacker Burghausen | - | Stuttgarter Kickers | 2:0 | ||||
| 3. Round | 16/08/2008 | Wacker Burghausen | - | Fortuna Düsseldorf | 0:4 | ||||
| 6. Round | 13/09/2008 | Wuppertaler SV | - | Wacker Burghausen | 2:4 | ||||
| 9. Round | 04/10/2008 | Wacker Burghausen | - | Jahn Regensburg | 0:1 | ||||
| 10. Round | 18/10/2008 | Eintracht Braunschweig | - | Wacker Burghausen | 2:0 | ||||
| 11. Round | 25/10/2008 | Wacker Burghausen | - | Erzgebirge Aue | 0:4 | ||||
| 20. Round | 20/12/2008 | Stuttgarter Kickers | - | Wacker Burghausen | 0:0 | ||||
| 19. Round | 04/03/2009 | VfB Stuttgart II | - | Wacker Burghausen | 3:0 | ||||
| 21. Round | 10/03/2009 | Wacker Burghausen | - | Kickers Offenbach | 0:0 | ||||
| 23. Round | 18/03/2009 | Wacker Burghausen | - | 1. FC Union Berlin | 0:0 | ||||
| 27. Round | 22/03/2009 | Wacker Burghausen | - | Dynamo Dresden | 0:3 | ||||
| 28. Round | 28/03/2009 | Jahn Regensburg | - | Wacker Burghausen | 1:0 | ||||
| 30. Round | 04/04/2009 | Erzgebirge Aue | - | Wacker Burghausen | 2:0 |  |
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| 35. Round | 08/05/2009 | Wacker Burghausen | - | Werder Bremen II | 2:2 |
Germany