| 1. Round | 16/08/2008 | 1. FC Heidenheim 1846 | - | SC Pfullendorf | 1:2 | ||||
| 2. Round | 23/08/2008 | SSV Ulm 1846 | - | 1. FC Heidenheim 1846 | 0:0 | ||||
| 3. Round | 30/08/2008 | 1. FC Heidenheim 1846 | - | 1. FC Eintracht Bamberg | 5:4 |  |
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| 4. Round | 12/09/2008 | TSV 1860 München II | - | 1. FC Heidenheim 1846 | 0:3 | |
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| 5. Round | 20/09/2008 | 1. FC Heidenheim 1846 | - | Hessen Kassel | 0:0 | ||||
| 6. Round | 27/09/2008 | SC Freiburg II | - | 1. FC Heidenheim 1846 | 1:3 | |
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| 7. Round | 04/10/2008 | 1. FC Heidenheim 1846 | - | SpVgg Greuther Fürth II | 2:1 | |
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| 8. Round | 17/10/2008 | Waldhof Mannheim | - | 1. FC Heidenheim 1846 | 1:2 | ||||
| 18. Round | 15/04/2009 | SC Pfullendorf | - | 1. FC Heidenheim 1846 | 2:1 | ||||
| 28. Round | 02/05/2009 | 1. FC Heidenheim 1846 | - | Viktoria Aschaffenburg | 3:1 | ||||
| 29. Round | 10/05/2009 | TSV Großbardorf | - | 1. FC Heidenheim 1846 | 2:4 | ||||
| 19. Round | 26/05/2009 | 1. FC Heidenheim 1846 | - | SSV Ulm 1846 | 1:1 | ||||
| 33. Round | 30/05/2009 | Karlsruher SC II | - | 1. FC Heidenheim 1846 | 0:2 |
Germany