| 5. Round | 28/09/2008 | 1. FSV Mainz 05 [Youth B] | - | Kickers Offenbach [Youth B] | 2:0 |  |
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| 11. Round | 30/11/2008 | 1. FSV Mainz 05 [Youth B] | - | VfB Stuttgart [Youth B] | 0:2 | ||||
| 12. Round | 06/12/2008 | SC Freiburg [Youth B] | - | 1. FSV Mainz 05 [Youth B] | 2:1 | ||||
| 13. Round | 14/12/2008 | 1. FSV Mainz 05 [Youth B] | - | SpVgg Greuther Fürth [Youth B] | 0:0 | |
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| 15. Round | 21/02/2009 | 1899 Hoffenheim [Youth B] | - | 1. FSV Mainz 05 [Youth B] | 0:3 | |
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| 16. Round | 01/03/2009 | 1. FSV Mainz 05 [Youth B] | - | TSV 1860 München [Youth B] | 0:1 | ||||
| 17. Round | 07/03/2009 | SSV Ulm 1846 [Youth B] | - | 1. FSV Mainz 05 [Youth B] | 0:0 | |
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| 19. Round | 22/03/2009 | 1. FSV Mainz 05 [Youth B] | - | 1. FC Saarbrücken [Youth B] | 1:2 |  |
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| 20. Round | 05/04/2009 | 1. FC Kaiserslautern [Youth B] | - | 1. FSV Mainz 05 [Youth B] | 2:0 | |
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| 23. Round | 17/05/2009 | 1. FSV Mainz 05 [Youth B] | - | Bayern München [Youth B] | 2:3 | ||||
| 24. Round | 24/05/2009 | VfB Stuttgart [Youth B] | - | 1. FSV Mainz 05 [Youth B] | 5:2 | |
Germany