| 20. Round | 02/03/2013 | MŠK Žilina | - | FK Dukla Banská Bystrica | 0:1 | ||||
| 21. Round | 08/03/2013 | FK Dukla Banská Bystrica | - | Spartak Trnava | 2:0 |  |
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| 22. Round | 16/03/2013 | Slovan Bratislava | - | FK Dukla Banská Bystrica | 2:0 | ||||
| 23. Round | 30/03/2013 | FK Senica | - | FK Dukla Banská Bystrica | 1:1 | ||||
| 24. Round | 02/04/2013 | FK Dukla Banská Bystrica | - | AS Trenčín | 0:0 | ||||
| 25. Round | 06/04/2013 | MFK Ružomberok | - | FK Dukla Banská Bystrica | 3:2 | ||||
| 26. Round | 13/04/2013 | FK Dukla Banská Bystrica | - | Zlaté Moravce | 1:0 | ||||
| 28. Round | 27/04/2013 | Spartak Myjava | - | FK Dukla Banská Bystrica | 2:1 | ||||
| 29. Round | 04/05/2013 | FK Dukla Banská Bystrica | - | 1. FC Tatran Prešov | 0:0 | ||||
| 32. Round | 22/05/2013 | Spartak Trnava | - | FK Dukla Banská Bystrica | 0:1 |
Czech Republic