| 2. Round | 29/07/2009 | Holstein Kiel | - | Wacker Burghausen | 0:1 | ||||
| 3. Round | 08/08/2009 | Jahn Regensburg | - | Wacker Burghausen | 0:0 |  |
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| 4. Round | 15/08/2009 | Wacker Burghausen | - | Eintracht Braunschweig | 0:2 | ||||
| 5. Round | 22/08/2009 | Werder Bremen II | - | Wacker Burghausen | 3:4 | ||||
| 6. Round | 30/08/2009 | Wacker Burghausen | - | Kickers Offenbach | 1:0 | ||||
| 7. Round | 02/09/2009 | FC Ingolstadt 04 | - | Wacker Burghausen | 6:0 | ||||
| 9. Round | 12/09/2009 | FC Carl Zeiss Jena | - | Wacker Burghausen | 0:0 | ||||
| 11. Round | 26/09/2009 | 1. FC Heidenheim 1846 | - | Wacker Burghausen | 6:1 | ||||
| 12. Round | 03/10/2009 | Wacker Burghausen | - | Wuppertaler SV | 1:0 | ||||
| 13. Round | 18/10/2009 | VfB Stuttgart II | - | Wacker Burghausen | 1:0 | ||||
| 18. Round | 28/11/2009 | Wacker Burghausen | - | Rot-Weiß Erfurt | 1:3 | ||||
| 19. Round | 05/12/2009 | VfL Osnabrück | - | Wacker Burghausen | 2:1 | ||||
| 20. Round | 12/12/2009 | Borussia Dortmund II | - | Wacker Burghausen | 3:0 | ||||
| 21. Round | 10/02/2010 | Wacker Burghausen | - | Holstein Kiel | 0:3 | |
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| 25. Round | 20/02/2010 | Kickers Offenbach | - | Wacker Burghausen | 3:0 | |
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| 24. Round | 24/03/2010 | Wacker Burghausen | - | Werder Bremen II | 1:1 |
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