| 9. Round | 16/09/2012 | FK Dukla Banská Bystrica | - | MŠK Žilina | 2:2 |  |
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| 10. Round | 22/09/2012 | MŠK Žilina | - | 1. FC Tatran Prešov | 3:0 | ||||
| 11. Round | 29/09/2012 | MFK Košice | - | MŠK Žilina | 1:1 | ||||
| 12. Round | 06/10/2012 | Spartak Myjava | - | MŠK Žilina | 1:1 | ||||
| 13. Round | 20/10/2012 | Spartak Trnava | - | MŠK Žilina | 1:2 | ||||
| 14. Round | 28/10/2012 | MŠK Žilina | - | Slovan Bratislava | 0:0 | ||||
| 15. Round | 03/11/2012 | FK Senica | - | MŠK Žilina | 0:0 | ||||
| 16. Round | 11/11/2012 | MŠK Žilina | - | AS Trenčín | 0:0 | ||||
| 17. Round | 17/11/2012 | MFK Ružomberok | - | MŠK Žilina | 1:0 | ||||
| 18. Round | 23/11/2012 | MŠK Žilina | - | Zlaté Moravce | 4:1 |  |
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| 19. Round | 30/11/2012 | FC Nitra | - | MŠK Žilina | 2:0 | ||||
| 21. Round | 09/03/2013 | 1. FC Tatran Prešov | - | MŠK Žilina | 0:0 | ||||
| 22. Round | 17/03/2013 | MŠK Žilina | - | MFK Košice | 0:1 | ||||
| 24. Round | 02/04/2013 | MŠK Žilina | - | Spartak Trnava | 1:1 | |
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| 25. Round | 06/04/2013 | Slovan Bratislava | - | MŠK Žilina | 1:1 | ||||
| 26. Round | 13/04/2013 | MŠK Žilina | - | FK Senica | 0:1 |
Slovakia