| 17. Round | 01/03/2025 | Zbrojovka Brno | - | MFK Chrudim | 0:0 | ||||
| 18. Round | 08/03/2025 | MFK Chrudim | - | Slavia Praha B | 0:1 | ||||
| 21. Round | 06/04/2025 | AC Sparta Praha B | - | MFK Chrudim | 2:2 |  |
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| 22. Round | 12/04/2025 | MFK Chrudim | - | SFC Opava | 2:0 | ||||
| 23. Round | 16/04/2025 | MFK Chrudim | - | MFK Vyškov | 3:0 | |
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| 24. Round | 19/04/2025 | FK MAS Táborsko | - | MFK Chrudim | 1:2 | |
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| 25. Round | 26/04/2025 | MFK Chrudim | - | SK Líšeň | 1:1 | ||||
| 26. Round | 04/05/2025 | Viktoria Žižkov | - | MFK Chrudim | 1:2 | |
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| 27. Round | 07/05/2025 | MFK Chrudim | - | 1. SK Prostějov | 1:3 | |
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| 30. Round | 25/05/2025 | Sigma Olomouc B | - | MFK Chrudim | 3:1 |
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Ukraine