| 3. Round | 05/08/2006 | Würzburger FV | - | TSV Großbardorf | 2:0 | ||||
| 4. Round | 11/08/2006 | 1. FC Eintracht Bamberg | - | Würzburger FV | 2:1 | ||||
| 5. Round | 16/08/2006 | Würzburger FV | - | FC Memmingen | 2:1 | ||||
| 7. Round | 26/08/2006 | Würzburger FV | - | SV Heimstetten | 3:1 | ||||
| 8. Round | 30/08/2006 | TSV Aindling | - | Würzburger FV | 1:0 | ||||
| 10. Round | 08/09/2006 | Würzburger FV | - | 1. FC Nürnberg II | 4:0 | ||||
| 11. Round | 16/09/2006 | FC Ismaning | - | Würzburger FV | 3:0 | ||||
| 14. Round | 03/10/2006 | Würzburger FV | - | SC Fürstenfeldbruck | 1:0 | ||||
| 15. Round | 14/10/2006 | Jahn Regensburg | - | Würzburger FV | 3:0 | ||||
| 16. Round | 21/10/2006 | Würzburger FV | - | Wacker Burghausen II | 3:2 | ||||
| 17. Round | 28/10/2006 | SpVgg Bayern Hof | - | Würzburger FV | 2:0 | ||||
| 19. Round | 11/11/2006 | SpVgg Greuther Fürth II | - | Würzburger FV | 2:0 | ||||
| 21. Round | 25/11/2006 | Würzburger FV | - | 1. FC Bad Kötzting | 1:2 | ||||
| 23. Round | 09/12/2006 | Würzburger FV | - | 1. FC Eintracht Bamberg | 1:4 |
Germany