| 1. Round | 17/08/2008 | Hamburger SV II | - | VFC Plauen | 1:1 | ||||
| 3. Round | 31/08/2008 | Hamburger SV II | - | VfB Lübeck | 2:1 |  |
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| 16. Round | 09/12/2008 | Hamburger SV II | - | Hertha BSC II | 1:1 | ||||
| 18. Round | 20/12/2008 | VFC Plauen | - | Hamburger SV II | 3:2 | |
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| 20. Round | 28/02/2009 | VfB Lübeck | - | Hamburger SV II | 1:0 | ||||
| 21. Round | 07/03/2009 | Hamburger SV II | - | SV Wilhelmshaven | 2:0 | |
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| 22. Round | 15/03/2009 | 1. FC Magdeburg | - | Hamburger SV II | 2:1 |  |
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| 23. Round | 21/03/2009 | Hamburger SV II | - | Energie Cottbus II | 0:1 | ||||
| 25. Round | 05/04/2009 | Hamburger SV II | - | Türkiyemspor Berlin | 0:0 | ||||
| 19. Round | 10/04/2009 | Hamburger SV II | - | Sachsen Leipzig | 4:0 | |
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| 26. Round | 19/04/2009 | FC Oberneuland | - | Hamburger SV II | 0:3 | |
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| 27. Round | 26/04/2009 | Hamburger SV II | - | Chemnitzer FC | 2:2 | ||||
| 29. Round | 10/05/2009 | Hamburger SV II | - | Holstein Kiel | 0:2 | |
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| 30. Round | 13/05/2009 | SV Babelsberg 03 | - | Hamburger SV II | 6:1 | |
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| 31. Round | 17/05/2009 | Hamburger SV II | - | Hallescher FC | 1:1 | ||||
| 33. Round | 30/05/2009 | Hertha BSC II | - | Hamburger SV II | 0:2 | |
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| 34. Round | 07/06/2009 | Hamburger SV II | - | VfL Wolfsburg II | 2:1 | |
Germany