| 17. Round | 03/03/2025 | FC Zlín | - | 1. SK Prostějov | 3:0 | ||||
| 18. Round | 07/03/2025 | 1. SK Prostějov | - | Viktoria Žižkov | 2:1 | ||||
| 19. Round | 14/03/2025 | FC Sellier & Bellot Vlašim | - | 1. SK Prostějov | 3:1 | ||||
| 20. Round | 28/03/2025 | 1. SK Prostějov | - | Baník Ostrava B | 1:0 | ||||
| 21. Round | 04/04/2025 | Vysočina Jihlava | - | 1. SK Prostějov | 3:0 | ||||
| 26. Round | 03/05/2025 | 1. SK Prostějov | - | AC Sparta Praha B | 1:2 |  |
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| 27. Round | 07/05/2025 | MFK Chrudim | - | 1. SK Prostějov | 1:3 | ||||
| 28. Round | 11/05/2025 | 1. SK Prostějov | - | SK Líšeň | 1:0 | ||||
| 29. Round | 17/05/2025 | FK MAS Táborsko | - | 1. SK Prostějov | 1:0 | ||||
| 30. Round | 25/05/2025 | 1. SK Prostějov | - | MFK Vyškov | 0:2 |
Czech Republic