| 12. Round | 06/10/2024 | FK Varnsdorf | - | FC Zlín | 0:2 | ||||
| 13. Round | 18/10/2024 | Vysočina Jihlava | - | FK Varnsdorf | 1:1 | ||||
| 14. Round | 27/10/2024 | FK Varnsdorf | - | FC Sellier & Bellot Vlašim | 1:2 | ||||
| 15. Round | 03/11/2024 | Slavia Praha B | - | FK Varnsdorf | 2:1 | ||||
| 16. Round | 10/11/2024 | FK Varnsdorf | - | Baník Ostrava B | 0:0 |  |
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| 17. Round | 01/03/2025 | SFC Opava | - | FK Varnsdorf | 0:1 | ||||
| 18. Round | 09/03/2025 | FK Varnsdorf | - | Zbrojovka Brno | 0:3 | ||||
| 19. Round | 16/03/2025 | FK Varnsdorf | - | AC Sparta Praha B | 2:1 | ||||
| 20. Round | 29/03/2025 | MFK Chrudim | - | FK Varnsdorf | 2:1 |  |
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| 21. Round | 06/04/2025 | FK Varnsdorf | - | SK Líšeň | 2:1 | |
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| 22. Round | 12/04/2025 | MFK Vyškov | - | FK Varnsdorf | 2:2 | ||||
| 23. Round | 16/04/2025 | FK Varnsdorf | - | FK MAS Táborsko | 1:2 | ||||
| 27. Round | 07/05/2025 | FK Varnsdorf | - | Vysočina Jihlava | 2:2 | ||||
| 28. Round | 11/05/2025 | FC Sellier & Bellot Vlašim | - | FK Varnsdorf | 1:1 | ||||
| 29. Round | 17/05/2025 | FK Varnsdorf | - | Slavia Praha B | 3:0 | |
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| 30. Round | 25/05/2025 | Viktoria Žižkov | - | FK Varnsdorf | 6:2 |
Czech Republic