| 1. Round | 14/07/2012 | Spartak Trnava | - | MFK Košice | 0:0 | ||||
| 2. Round | 22/07/2012 | MFK Košice | - | Slovan Bratislava | 1:0 |  |
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| 3. Round | 29/07/2012 | FK Senica | - | MFK Košice | 2:1 | ||||
| 4. Round | 04/08/2012 | MFK Košice | - | AS Trenčín | 3:0 | ||||
| 5. Round | 11/08/2012 | MFK Ružomberok | - | MFK Košice | 3:1 | |
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| 7. Round | 25/08/2012 | FC Nitra | - | MFK Košice | 4:1 | ||||
| 8. Round | 01/09/2012 | MFK Košice | - | FK Dukla Banská Bystrica | 1:0 | ||||
| 9. Round | 15/09/2012 | 1. FC Tatran Prešov | - | MFK Košice | 0:0 | ||||
| 12. Round | 05/10/2012 | MFK Košice | - | Spartak Trnava | 1:0 | ||||
| 13. Round | 21/10/2012 | Slovan Bratislava | - | MFK Košice | 3:1 | ||||
| 17. Round | 16/11/2012 | Zlaté Moravce | - | MFK Košice | 1:0 | ||||
| 21. Round | 09/03/2013 | MFK Košice | - | Spartak Myjava | 1:2 | ||||
| 27. Round | 20/04/2013 | MFK Ružomberok | - | MFK Košice | 1:1 | ||||
| 28. Round | 27/04/2013 | MFK Košice | - | Zlaté Moravce | 0:2 | ||||
| 30. Round | 11/05/2013 | MFK Košice | - | FK Dukla Banská Bystrica | 1:0 | ||||
| 29. Round | 14/05/2013 | FC Nitra | - | MFK Košice | 1:0 | ||||
| 31. Round | 18/05/2013 | 1. FC Tatran Prešov | - | MFK Košice | 0:0 | ||||
| 33. Round | 26/05/2013 | MFK Košice | - | MŠK Žilina | 2:2 |
Slovakia