| 1. Round | 29/07/2016 | FK Dukla Praha | - | FK Teplice | 0:1 | ||||
| 2. Round | 06/08/2016 | 1. FC Slovácko | - | FK Dukla Praha | 2:2 | ||||
| 3. Round | 14/08/2016 | FK Dukla Praha | - | FC Hradec Králové | 3:0 | ||||
| 4. Round | 20/08/2016 | MFK Karviná | - | FK Dukla Praha | 2:1 | ||||
| 5. Round | 28/08/2016 | FK Dukla Praha | - | AC Sparta Praha | 0:2 | ||||
| 6. Round | 11/09/2016 | FK Jablonec | - | FK Dukla Praha | 1:1 |  |
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| 7. Round | 17/09/2016 | FK Dukla Praha | - | Bohemians Praha 1905 | 4:1 | ||||
| 8. Round | 24/09/2016 | FK Dukla Praha | - | Zbrojovka Brno | 4:2 | ||||
| 9. Round | 01/10/2016 | FK Mladá Boleslav | - | FK Dukla Praha | 1:0 | ||||
| 10. Round | 15/10/2016 | FK Dukla Praha | - | Slovan Liberec | 0:0 | ||||
| 11. Round | 21/10/2016 | Vysočina Jihlava | - | FK Dukla Praha | 1:1 | ||||
| 12. Round | 30/10/2016 | FK Dukla Praha | - | Viktoria Plzeň | 0:1 | ||||
| 13. Round | 05/11/2016 | 1. FK Příbram | - | FK Dukla Praha | 3:1 | |
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| 14. Round | 18/11/2016 | FK Dukla Praha | - | Slavia Praha | 1:2 |  |
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| 15. Round | 26/11/2016 | FC Fastav Zlín | - | FK Dukla Praha | 0:1 | ||||
| 16. Round | 04/12/2016 | FK Dukla Praha | - | 1. FC Slovácko | 2:3 |
Bosnia-Herzegovina