| 1. Round | 21/07/2012 | Wacker Burghausen | - | Preußen Münster | 0:2 | ||||
| 2. Round | 28/07/2012 | Alemannia Aachen | - | Wacker Burghausen | 3:2 | ||||
| 3. Round | 04/08/2012 | Wacker Burghausen | - | Chemnitzer FC | 2:1 | ||||
| 4. Round | 07/08/2012 | Borussia Dortmund II | - | Wacker Burghausen | 2:1 | ||||
| 6. Round | 25/08/2012 | 1. FC Saarbrücken | - | Wacker Burghausen | 3:0 | ||||
| 8. Round | 01/09/2012 | Kickers Offenbach | - | Wacker Burghausen | 1:0 | ||||
| 9. Round | 15/09/2012 | Wacker Burghausen | - | SV Wehen Wiesbaden | 0:0 | ||||
| 15. Round | 27/10/2012 | Wacker Burghausen | - | VfB Stuttgart II | 1:3 | ||||
| 16. Round | 02/11/2012 | SpVgg Unterhaching | - | Wacker Burghausen | 3:0 | ||||
| 17. Round | 10/11/2012 | Wacker Burghausen | - | VfL Osnabrück | 1:1 | ||||
| 18. Round | 17/11/2012 | Wacker Burghausen | - | SV Babelsberg 03 | 3:1 | ||||
| 19. Round | 24/11/2012 | Arminia Bielefeld | - | Wacker Burghausen | 3:0 | ||||
| 20. Round | 01/12/2012 | Preußen Münster | - | Wacker Burghausen | 2:0 |
Austria