| 1. Round | 15/08/2008 | 1. FSV Mainz 05 | - | 1. FC Kaiserslautern | 3:3 | ||||
| 2. Round | 24/08/2008 | TSV 1860 München | - | 1. FSV Mainz 05 | 1:2 | ||||
| 3. Round | 29/08/2008 | 1. FSV Mainz 05 | - | VfL Osnabrück | 4:2 | ||||
| 4. Round | 14/09/2008 | Hansa Rostock | - | 1. FSV Mainz 05 | 2:2 | ||||
| 5. Round | 19/09/2008 | 1. FSV Mainz 05 | - | 1. FC Nürnberg | 2:0 | ||||
| 6. Round | 28/09/2008 | FC Augsburg | - | 1. FSV Mainz 05 | 0:2 | ||||
| 7. Round | 06/10/2008 | 1. FSV Mainz 05 | - | SV Wehen Wiesbaden | 5:0 |  |
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| 8. Round | 20/10/2008 | Alemannia Aachen | - | 1. FSV Mainz 05 | 2:0 | ||||
| 9. Round | 26/10/2008 | 1. FSV Mainz 05 | - | MSV Duisburg | 0:0 | ||||
| 10. Round | 29/10/2008 | SC Freiburg | - | 1. FSV Mainz 05 | 0:1 | ||||
| 13. Round | 16/11/2008 | TuS Koblenz | - | 1. FSV Mainz 05 | 0:3 | ||||
| 14. Round | 23/11/2008 | 1. FSV Mainz 05 | - | FC St. Pauli | 2:2 | ||||
| 15. Round | 01/12/2008 | FSV Frankfurt | - | 1. FSV Mainz 05 | 1:4 | ||||
| 16. Round | 05/12/2008 | 1. FSV Mainz 05 | - | SpVgg Greuther Fürth | 0:1 | ||||
| 17. Round | 14/12/2008 | Rot-Weiß Oberhausen | - | 1. FSV Mainz 05 | 2:1 | ||||
| 18. Round | 02/02/2009 | 1. FC Kaiserslautern | - | 1. FSV Mainz 05 | 1:1 |  |
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| 19. Round | 08/02/2009 | 1. FSV Mainz 05 | - | TSV 1860 München | 2:2 |
Belgium