| 8. Round | 10/09/2016 | MFK Zemplín Michalovce | - | MŠK Žilina | 0:2 |  |
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| 9. Round | 17/09/2016 | MŠK Žilina | - | FK Senica | 4:2 | ||||
| 10. Round | 24/09/2016 | Zlaté Moravce | - | MŠK Žilina | 0:2 | ||||
| 19. Round | 11/12/2016 | MŠK Žilina | - | MFK Zemplín Michalovce | 7:1 | |
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| 20. Round | 18/02/2017 | FK Senica | - | MŠK Žilina | 2:0 |  |
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| 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 | |
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| 24. Round | 18/03/2017 | MŠK Žilina | - | MFK Ružomberok | 3:1 | |
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| 26. Round | 09/04/2017 | Spartak Trnava | - | MŠK Žilina | 1:2 | ||||
| 29. Round | 28/04/2017 | AS Trenčín | - | MŠK Žilina | 2:1 | ||||
| 30. Round | 06/05/2017 | MFK Zemplín Michalovce | - | MŠK Žilina | 0:1 | ||||
| 32. Round | 19/05/2017 | Zlaté Moravce | - | MŠK Žilina | 1:4 |
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