| 1. Round | 06/08/2016 | SV Sandhausen | - | Fortuna Düsseldorf | 2:2 |  |
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| 2. Round | 12/08/2016 | Fortuna Düsseldorf | - | VfB Stuttgart | 1:0 | ||||
| 4. Round | 11/09/2016 | Fortuna Düsseldorf | - | SpVgg Greuther Fürth | 1:1 | |
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| 5. Round | 17/09/2016 | 1. FC Heidenheim 1846 | - | Fortuna Düsseldorf | 2:0 | |
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| 6. Round | 20/09/2016 | Fortuna Düsseldorf | - | VfL Bochum | 3:0 | ||||
| 7. Round | 23/09/2016 | Eintracht Braunschweig | - | Fortuna Düsseldorf | 2:1 | |
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| 8. Round | 01/10/2016 | Fortuna Düsseldorf | - | Karlsruher SC | 1:1 | ||||
| 18. Round | 27/01/2017 | Fortuna Düsseldorf | - | SV Sandhausen | 0:3 | ||||
| 19. Round | 06/02/2017 | VfB Stuttgart | - | Fortuna Düsseldorf | 2:0 | |
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| 26. Round | 31/03/2017 | Fortuna Düsseldorf | - | TSV 1860 München | 0:1 | ||||
| 27. Round | 04/04/2017 | Arminia Bielefeld | - | Fortuna Düsseldorf | 2:1 | |
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| 30. Round | 21/04/2017 | Fortuna Düsseldorf | - | FC St. Pauli | 1:3 | ||||
| 31. Round | 30/04/2017 | Hannover 96 | - | Fortuna Düsseldorf | 1:0 | |
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| 32. Round | 06/05/2017 | Fortuna Düsseldorf | - | Würzburger Kickers | 1:1 | ||||
| 33. Round | 14/05/2017 | 1. FC Nürnberg | - | Fortuna Düsseldorf | 2:3 |
Germany