| 3. Jornada | 30.07.2016 | FK Senica | - | MFK Zemplín Michalovce | 2:0 |  |
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| 6. Jornada | 20.08.2016 | FK Senica | - | FO ŽP Šport Podbrezová | 0:1 | ||||
| 7. Jornada | 25.08.2016 | FC DAC 1904 | - | FK Senica | 0:0 | |
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| 11. Jornada | 01.10.2016 | Spartak Myjava | - | FK Senica | anu. | ||||
| 12. Jornada | 16.10.2016 | Slovan Bratislava | - | FK Senica | 2:0 | ||||
| 13. Jornada | 22.10.2016 | FK Senica | - | AS Trenčín | 1:2 | |
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| 14. Jornada | 29.10.2016 | MFK Zemplín Michalovce | - | FK Senica | 0:0 | ||||
| 15. Jornada | 05.11.2016 | FK Senica | - | 1. FC Tatran Prešov | 0:0 | ||||
| 16. Jornada | 19.11.2016 | FK Senica | - | Zlaté Moravce | 1:3 | ||||
| 17. Jornada | 26.11.2016 | FO ŽP Šport Podbrezová | - | FK Senica | 2:0 | ||||
| 18. Jornada | 03.12.2016 | FK Senica | - | FC DAC 1904 | 1:1 | ||||
| 19. Jornada | 10.12.2016 | MFK Ružomberok | - | FK Senica | 2:1 |  |
Eslovaquia