| 1. Round | 15/07/2012 | FK Senica | - | FK Dukla Banská Bystrica | 2:3 | ||||
| 2. Round | 22/07/2012 | 1. FC Tatran Prešov | - | FK Senica | 2:0 | ||||
| 3. Round | 29/07/2012 | FK Senica | - | MFK Košice | 2:1 | ||||
| 5. Round | 12/08/2012 | FK Senica | - | Spartak Trnava | 3:0 | ||||
| 6. Round | 19/08/2012 | Slovan Bratislava | - | FK Senica | 1:0 | ||||
| 7. Round | 24/08/2012 | FK Senica | - | Spartak Myjava | 0:1 | ||||
| 9. Round | 15/09/2012 | MFK Ružomberok | - | FK Senica | 0:2 |  |
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| 10. Round | 22/09/2012 | FK Senica | - | Zlaté Moravce | 3:0 | ||||
| 11. Round | 30/09/2012 | FC Nitra | - | FK Senica | 0:1 | ||||
| 12. Round | 06/10/2012 | FK Dukla Banská Bystrica | - | FK Senica | 1:2 | ||||
| 13. Round | 20/10/2012 | FK Senica | - | 1. FC Tatran Prešov | 2:0 | ||||
| 16. Round | 10/11/2012 | Spartak Trnava | - | FK Senica | 1:1 | ||||
| 17. Round | 17/11/2012 | FK Senica | - | Slovan Bratislava | 0:1 | ||||
| 18. Round | 25/11/2012 | Spartak Myjava | - | FK Senica | 1:2 | ||||
| 19. Round | 02/12/2012 | AS Trenčín | - | FK Senica | 1:1 |
Czech Republic