| 6. Round | 19/08/2006 | 1. FC Bad Kötzting | - | VfL Frohnlach | 1:0 |  |
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| 7. Round | 25/08/2006 | SC Fürstenfeldbruck | - | 1. FC Bad Kötzting | 2:1 | ||||
| 8. Round | 30/08/2006 | 1. FC Bad Kötzting | - | Jahn Regensburg | 3:0 | ||||
| 9. Round | 02/09/2006 | Wacker Burghausen II | - | 1. FC Bad Kötzting | 1:3 | ||||
| 10. Round | 09/09/2006 | 1. FC Bad Kötzting | - | SpVgg Bayern Hof | 4:3 | ||||
| 11. Round | 16/09/2006 | SpVgg Unterhaching II | - | 1. FC Bad Kötzting | 3:0 | ||||
| 12. Round | 23/09/2006 | 1. FC Bad Kötzting | - | SpVgg Greuther Fürth II | 0:1 | ||||
| 13. Round | 29/09/2006 | SpVgg Weiden | - | 1. FC Bad Kötzting | 3:0 | ||||
| 26. Round | 10/03/2007 | 1. FC Bad Kötzting | - | SC Fürstenfeldbruck | 6:1 | ||||
| 27. Round | 17/03/2007 | Jahn Regensburg | - | 1. FC Bad Kötzting | 4:1 | ||||
| 31. Round | 14/04/2007 | SpVgg Greuther Fürth II | - | 1. FC Bad Kötzting | 3:1 |
Germany