| 7. Round | 28/08/2016 | MŠK Žilina | - | AS Trenčín | 4:0 |  |
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| 10. Round | 24/09/2016 | Zlaté Moravce | - | MŠK Žilina | 0:2 | ||||
| 11. Round | 01/10/2016 | MŠK Žilina | - | FO ŽP Šport Podbrezová | 1:0 | ||||
| 12. Round | 15/10/2016 | FC DAC 1904 | - | MŠK Žilina | 0:6 | ||||
| 13. Round | 22/10/2016 | MFK Ružomberok | - | MŠK Žilina | 0:2 | ||||
| 14. Round | 30/10/2016 | 1. FC Tatran Prešov | - | MŠK Žilina | 1:1 | ||||
| 15. Round | 06/11/2016 | MŠK Žilina | - | Spartak Trnava | 7:0 | ||||
| 16. Round | 20/11/2016 | Spartak Myjava | - | MŠK Žilina | annull. | ||||
| 17. Round | 26/11/2016 | MŠK Žilina | - | Slovan Bratislava | 2:1 | ||||
| 20. Round | 18/02/2017 | FK Senica | - | MŠK Žilina | 2:0 | ||||
| 21. Round | 26/02/2017 | MŠK Žilina | - | Zlaté Moravce | 4:1 | ||||
| 22. Round | 05/03/2017 | FO ŽP Šport Podbrezová | - | MŠK Žilina | 2:2 | ||||
| 23. Round | 11/03/2017 | FC DAC 1904 | - | MŠK Žilina | 2:2 | ||||
| 25. Round | 02/04/2017 | MŠK Žilina | - | 1. FC Tatran Prešov | 3:0 | ||||
| 26. Round | 09/04/2017 | Spartak Trnava | - | MŠK Žilina | 1:2 | ||||
| 28. Round | 23/04/2017 | Slovan Bratislava | - | MŠK Žilina | 0:1 | ||||
| 29. Round | 28/04/2017 | AS Trenčín | - | MŠK Žilina | 2:1 | ||||
| 31. Round | 13/05/2017 | MŠK Žilina | - | FK Senica | 3:2 |
Slovakia