| 3. Round | 28/07/2012 | Viktoria Aschaffenburg | - | Würzburger Kickers | 0:3 | ||||
| 4. Round | 03/08/2012 | Würzburger Kickers | - | TSV 1896 Rain | 3:2 | ||||
| 6. Round | 10/08/2012 | Würzburger Kickers | - | FV Illertissen | 1:3 | ||||
| 7. Round | 15/08/2012 | Würzburger Kickers | - | FC Augsburg II | 4:2 | ||||
| 10. Round | 01/09/2012 | TSV 1860 München II | - | Würzburger Kickers | 6:2 | ||||
| 14. Round | 29/09/2012 | TSV 1860 Rosenheim | - | Würzburger Kickers | 1:2 | ||||
| 19. Round | 27/10/2012 | Würzburger Kickers | - | Bayern München II | 2:1 |  |
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| 20. Round | 03/11/2012 | Würzburger Kickers | - | FC Ismaning | 0:5 | |
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| 21. Round | 10/11/2012 | SpVgg Greuther Fürth II | - | Würzburger Kickers | 3:1 | ||||
| 22. Round | 17/11/2012 | Würzburger Kickers | - | Viktoria Aschaffenburg | 1:1 | ||||
| 24. Round | 01/12/2012 | Würzburger Kickers | - | SV Seligenporten | 3:2 | ||||
| 37. Round | 18/05/2013 | Würzburger Kickers | - | Eintracht Bamberg | 0:2 |
Germany