| 2. Round | 28/07/2012 | Alemannia Aachen | - | Wacker Burghausen | 3:2 | ||||
| 4. Round | 07/08/2012 | Borussia Dortmund II | - | Wacker Burghausen | 2:1 | ||||
| 7. Round | 29/08/2012 | Wacker Burghausen | - | Hansa Rostock | 2:0 | ||||
| 8. Round | 01/09/2012 | Kickers Offenbach | - | Wacker Burghausen | 1:0 |  |
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| 10. Round | 22/09/2012 | Karlsruher SC | - | Wacker Burghausen | 1:2 | ||||
| 11. Round | 26/09/2012 | Wacker Burghausen | - | 1. FC Heidenheim 1846 | 4:1 | ||||
| 12. Round | 29/09/2012 | Rot-Weiß Erfurt | - | Wacker Burghausen | 0:3 | ||||
| 13. Round | 06/10/2012 | Wacker Burghausen | - | Hallescher FC | 2:0 | ||||
| 14. Round | 20/10/2012 | Stuttgarter Kickers | - | Wacker Burghausen | 1:2 | |
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| 15. Round | 27/10/2012 | Wacker Burghausen | - | VfB Stuttgart II | 1:3 |
Germany