| 1. Round | 17/08/2008 | Rot Weiss Ahlen | - | FSV Frankfurt | 2:1 | ||||
| 9. Round | 24/10/2008 | FSV Frankfurt | - | Hansa Rostock | 0:0 |  |
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| 10. Round | 28/10/2008 | FC Augsburg | - | FSV Frankfurt | 2:2 | |
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| 11. Round | 31/10/2008 | FSV Frankfurt | - | Alemannia Aachen | 0:3 | ||||
| 12. Round | 07/11/2008 | 1. FC Nürnberg | - | FSV Frankfurt | 0:0 | ||||
| 13. Round | 16/11/2008 | FSV Frankfurt | - | SC Freiburg | 1:2 | ||||
| 14. Round | 21/11/2008 | MSV Duisburg | - | FSV Frankfurt | 0:0 | ||||
| 23. Round | 06/03/2009 | FSV Frankfurt | - | 1. FC Kaiserslautern | 1:0 | ||||
| 24. Round | 13/03/2009 | TSV 1860 München | - | FSV Frankfurt | 1:1 | ||||
| 25. Round | 20/03/2009 | FSV Frankfurt | - | SV Wehen Wiesbaden | 2:1 |
Czech Republic