| 1. Round | 14/07/2012 | Spartak Trnava | - | MFK Košice | 0:0 |  |
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| 6. Round | 18/08/2012 | Spartak Trnava | - | AS Trenčín | 0:3 | ||||
| 2. Round | 21/08/2012 | MŠK Žilina | - | Spartak Trnava | 1:1 | ||||
| 7. Round | 25/08/2012 | MFK Ružomberok | - | Spartak Trnava | 2:2 | ||||
| 12. Round | 05/10/2012 | MFK Košice | - | Spartak Trnava | 1:0 | ||||
| 19. Round | 01/12/2012 | Zlaté Moravce | - | Spartak Trnava | 1:1 | ||||
| 20. Round | 02/03/2013 | Spartak Trnava | - | FC Nitra | 2:0 |  |
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| 21. Round | 08/03/2013 | FK Dukla Banská Bystrica | - | Spartak Trnava | 2:0 |  |
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| 22. Round | 16/03/2013 | Spartak Trnava | - | 1. FC Tatran Prešov | 2:1 | ||||
| 23. Round | 30/03/2013 | Spartak Trnava | - | MFK Košice | 2:3 | |
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| 24. Round | 02/04/2013 | MŠK Žilina | - | Spartak Trnava | 1:1 | ||||
| 25. Round | 06/04/2013 | Spartak Trnava | - | Spartak Myjava | 1:1 | |
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| 27. Round | 21/04/2013 | FK Senica | - | Spartak Trnava | 3:2 | ||||
| 28. Round | 27/04/2013 | Spartak Trnava | - | AS Trenčín | 2:0 | ||||
| 29. Round | 04/05/2013 | MFK Ružomberok | - | Spartak Trnava | 1:0 | ||||
| 32. Round | 22/05/2013 | Spartak Trnava | - | FK Dukla Banská Bystrica | 0:1 |
Czech Republic