| 1. Round | 14/07/2012 | AS Trenčín | - | FC Nitra | 5:0 |  |
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| 2. Round | 21/07/2012 | FC Nitra | - | MFK Ružomberok | 1:1 | ||||
| 3. Round | 28/07/2012 | Zlaté Moravce | - | FC Nitra | 0:2 | ||||
| 4. Round | 04/08/2012 | Spartak Myjava | - | FC Nitra | 0:2 | ||||
| 5. Round | 11/08/2012 | FC Nitra | - | FK Dukla Banská Bystrica | 1:1 | ||||
| 6. Round | 18/08/2012 | 1. FC Tatran Prešov | - | FC Nitra | 1:0 | ||||
| 7. Round | 25/08/2012 | FC Nitra | - | MFK Košice | 4:1 | ||||
| 8. Round | 01/09/2012 | MŠK Žilina | - | FC Nitra | 1:1 | ||||
| 9. Round | 14/09/2012 | FC Nitra | - | Spartak Trnava | 1:3 |  |
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| 11. Round | 30/09/2012 | FC Nitra | - | FK Senica | 0:1 | ||||
| 12. Round | 06/10/2012 | FC Nitra | - | AS Trenčín | 1:2 | |
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| 13. Round | 20/10/2012 | MFK Ružomberok | - | FC Nitra | 2:1 | ||||
| 14. Round | 27/10/2012 | FC Nitra | - | Zlaté Moravce | 1:1 | ||||
| 15. Round | 03/11/2012 | FC Nitra | - | Spartak Myjava | 0:2 | ||||
| 16. Round | 10/11/2012 | FK Dukla Banská Bystrica | - | FC Nitra | 2:0 | |
Slovakia