| 1. Round | 21/07/2012 | FC Ismaning | - | Würzburger Kickers | 2:0 | ||||
| 2. Round | 25/07/2012 | Würzburger Kickers | - | SpVgg Greuther Fürth II | 2:2 | ||||
| 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 | ||||
| 9. Round | 24/08/2012 | Würzburger Kickers | - | SV Heimstetten | 1:1 | ||||
| 11. Round | 08/09/2012 | Würzburger Kickers | - | SC Eltersdorf | 1:2 |  |
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| 12. Round | 14/09/2012 | FC Memmingen | - | Würzburger Kickers | 1:3 | ||||
| 13. Round | 22/09/2012 | Würzburger Kickers | - | FC Ingolstadt 04 II | 2:1 | ||||
| 14. Round | 29/09/2012 | TSV 1860 Rosenheim | - | Würzburger Kickers | 1:2 | ||||
| 17. Round | 13/10/2012 | Würzburger Kickers | - | VfL Frohnlach | 1:1 | ||||
| 27. Round | 09/03/2013 | Würzburger Kickers | - | SpVgg Bayern Hof | 1:1 | ||||
| 38. Round | 24/05/2013 | Bayern München II | - | Würzburger Kickers | 6:1 |
Germany