| 1. Round | 26/07/2008 | Wacker Burghausen | - | Stuttgarter Kickers | 2:0 | ||||
| 2. Round | 02/08/2008 | Kickers Offenbach | - | Wacker Burghausen | 2:0 | ||||
| 3. Round | 16/08/2008 | Wacker Burghausen | - | Fortuna Düsseldorf | 0:4 | ||||
| 4. Round | 22/08/2008 | 1. FC Union Berlin | - | Wacker Burghausen | 4:0 | ||||
| 5. Round | 30/08/2008 | Wacker Burghausen | - | SpVgg Unterhaching | 5:1 | ||||
| 6. Round | 13/09/2008 | Wuppertaler SV | - | Wacker Burghausen | 2:4 |  |
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| 7. Round | 20/09/2008 | Wacker Burghausen | - | SV Sandhausen | 2:3 | |
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| 8. Round | 27/09/2008 | Dynamo Dresden | - | Wacker Burghausen | 3:1 | ||||
| 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 | ||||
| 12. Round | 28/10/2008 | FC Carl Zeiss Jena | - | Wacker Burghausen | 2:2 |
Germany