| 1. Round | 25/07/2009 | 1. FC Heidenheim 1846 | - | Wuppertaler SV | 2:2 | ||||
| 2. Round | 29/07/2009 | VfB Stuttgart II | - | 1. FC Heidenheim 1846 | 1:1 | ||||
| 3. Round | 08/08/2009 | 1. FC Heidenheim 1846 | - | SV Wehen Wiesbaden | 0:2 |  |
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| 5. Round | 22/08/2009 | 1. FC Heidenheim 1846 | - | Bayern München II | 4:2 | ||||
| 8. Round | 05/09/2009 | VfL Osnabrück | - | 1. FC Heidenheim 1846 | 3:2 | |
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| 9. Round | 12/09/2009 | 1. FC Heidenheim 1846 | - | Borussia Dortmund II | 2:1 | ||||
| 10. Round | 19/09/2009 | Holstein Kiel | - | 1. FC Heidenheim 1846 | 1:0 | ||||
| 13. Round | 17/10/2009 | 1. FC Heidenheim 1846 | - | Werder Bremen II | 1:2 | ||||
| 14. Round | 24/10/2009 | Kickers Offenbach | - | 1. FC Heidenheim 1846 | 2:1 | ||||
| 15. Round | 31/10/2009 | 1. FC Heidenheim 1846 | - | FC Ingolstadt 04 | 0:1 | ||||
| 32. Round | 03/04/2010 | Werder Bremen II | - | 1. FC Heidenheim 1846 | 1:1 | ||||
| 34. Round | 14/04/2010 | FC Ingolstadt 04 | - | 1. FC Heidenheim 1846 | 4:3 |
Germany