| 2. Round | 23/07/2016 | MŠK Žilina | - | MFK Ružomberok | 3:2 |  |
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| 3. Round | 30/07/2016 | MŠK Žilina | - | 1. FC Tatran Prešov | 4:0 | |
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| 4. Round | 07/08/2016 | Spartak Trnava | - | MŠK Žilina | 1:2 | |
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| 5. Round | 13/08/2016 | MŠK Žilina | - | Spartak Myjava | annull. | ||||
| 6. Round | 20/08/2016 | Slovan Bratislava | - | MŠK Žilina | 1:0 | ||||
| 7. Round | 28/08/2016 | MŠK Žilina | - | AS Trenčín | 4:0 | |
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| 8. Round | 10/09/2016 | MFK Zemplín Michalovce | - | MŠK Žilina | 0:2 | ||||
| 9. Round | 17/09/2016 | MŠK Žilina | - | FK Senica | 4:2 | ||||
| 10. Round | 24/09/2016 | Zlaté Moravce | - | MŠK Žilina | 0:2 | |
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| 11. Round | 01/10/2016 | MŠK Žilina | - | FO ŽP Šport Podbrezová | 1:0 | |
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| 12. Round | 15/10/2016 | FC DAC 1904 | - | MŠK Žilina | 0:6 | |
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| 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 | ||||
| 30. Round | 06/05/2017 | MFK Zemplín Michalovce | - | MŠK Žilina | 0:1 | ||||
| 31. Round | 13/05/2017 | MŠK Žilina | - | FK Senica | 3:2 | |
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| 32. Round | 19/05/2017 | Zlaté Moravce | - | MŠK Žilina | 1:4 | ||||
| 33. Round | 27/05/2017 | MŠK Žilina | - | FO ŽP Šport Podbrezová | 4:0 |
Nigeria