| 1. Round | 30/07/2016 | AC Sparta Praha | - | 1. FC Slovácko | 3:2 |  |
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| 2. Round | 06/08/2016 | 1. FC Slovácko | - | FK Dukla Praha | 2:2 |  |
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| 3. Round | 13/08/2016 | FK Jablonec | - | 1. FC Slovácko | 2:2 | ||||
| 4. Round | 20/08/2016 | 1. FC Slovácko | - | Bohemians Praha 1905 | 2:0 | |
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| 5. Round | 27/08/2016 | Zbrojovka Brno | - | 1. FC Slovácko | 1:0 | ||||
| 6. Round | 09/09/2016 | 1. FC Slovácko | - | FC Fastav Zlín | 1:3 | ||||
| 7. Round | 17/09/2016 | FK Mladá Boleslav | - | 1. FC Slovácko | 3:0 | ||||
| 8. Round | 24/09/2016 | 1. FC Slovácko | - | Vysočina Jihlava | 1:1 | |
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| 9. Round | 01/10/2016 | 1. FK Příbram | - | 1. FC Slovácko | 0:1 | ||||
| 10. Round | 15/10/2016 | 1. FC Slovácko | - | Viktoria Plzeň | 1:1 | |
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| 12. Round | 29/10/2016 | 1. FC Slovácko | - | FK Teplice | 1:1 | |
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| 13. Round | 06/11/2016 | MFK Karviná | - | 1. FC Slovácko | 0:1 | ||||
| 14. Round | 19/11/2016 | 1. FC Slovácko | - | FC Hradec Králové | 1:3 | |
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| 15. Round | 27/11/2016 | Slovan Liberec | - | 1. FC Slovácko | 2:2 | |
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| 16. Round | 04/12/2016 | FK Dukla Praha | - | 1. FC Slovácko | 2:3 |
Czech Republic