| 2. Round | 23/08/2008 | 1. FSV Mainz 05 II | - | Sportfreunde Lotte | 3:0 | ||||
| 6. Round | 26/09/2008 | 1. FSV Mainz 05 II | - | 1. FC Köln II | 2:3 | ||||
| 13. Round | 16/11/2008 | 1. FSV Mainz 05 II | - | 1. FC Kleve | 6:0 |  |
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| 14. Round | 02/12/2008 | Bor. Mönchengladbach II | - | 1. FSV Mainz 05 II | 1:0 | ||||
| 16. Round | 05/12/2008 | SV 07 Elversberg | - | 1. FSV Mainz 05 II | 3:0 | ||||
| 19. Round | 21/02/2009 | Sportfreunde Lotte | - | 1. FSV Mainz 05 II | 0:1 | |
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| 20. Round | 28/02/2009 | 1. FSV Mainz 05 II | - | FC Schalke 04 II | 2:0 | ||||
| 22. Round | 14/03/2009 | 1. FSV Mainz 05 II | - | VfL Bochum II | 2:3 |  |
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| 29. Round | 09/05/2009 | SC Verl | - | 1. FSV Mainz 05 II | 0:3 | ||||
| 31. Round | 16/05/2009 | 1. FSV Mainz 05 II | - | Bor. Mönchengladbach II | 1:2 | ||||
| 32. Round | 22/05/2009 | Bayer Leverkusen II | - | 1. FSV Mainz 05 II | 2:2 | |
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| 33. Round | 30/05/2009 | 1. FSV Mainz 05 II | - | SV 07 Elversberg | 0:1 | ||||
| 34. Round | 06/06/2009 | FSV Oggersheim | - | 1. FSV Mainz 05 II | 1:3 |
Germany