| 1. Round | 17/07/2016 | MŠK Žilina | - | FC DAC 1904 | 2:2 | ||||
| 2. Round | 23/07/2016 | MŠK Žilina | - | MFK Ružomberok | 3:2 | ||||
| 3. Round | 30/07/2016 | MŠK Žilina | - | 1. FC Tatran Prešov | 4:0 | ||||
| 8. Round | 10/09/2016 | MFK Zemplín Michalovce | - | MŠK Žilina | 0:2 | ||||
| 9. Round | 17/09/2016 | MŠK Žilina | - | FK Senica | 4:2 | ||||
| 11. Round | 01/10/2016 | MŠK Žilina | - | FO ŽP Šport Podbrezová | 1:0 | ||||
| 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 | ||||
| 18. Round | 03/12/2016 | MŠK Žilina | - | AS Trenčín | 3:0 | ||||
| 32. Round | 19/05/2017 | Zlaté Moravce | - | MŠK Žilina | 1:4 |
Slovakia