| 8. Jornada | 01.09.2024 | Zbrojovka Brno | - | FC Zlín | 1:2 | ||||
| 10. Jornada | 22.09.2024 | Baník Ostrava B | - | FC Zlín | 0:1 | ||||
| 14. Jornada | 26.10.2024 | MFK Vyškov | - | FC Zlín | 1:1 | ||||
| 15. Jornada | 04.11.2024 | FC Zlín | - | MFK Chrudim | 2:0 | ||||
| 16. Jornada | 09.11.2024 | FK MAS Táborsko | - | FC Zlín | 0:0 | ||||
| 17. Jornada | 03.03.2025 | FC Zlín | - | 1. SK Prostějov | 3:0 | ||||
| 18. Jornada | 09.03.2025 | Sigma Olomouc B | - | FC Zlín | 1:2 | ||||
| 19. Jornada | 16.03.2025 | Viktoria Žižkov | - | FC Zlín | 1:3 | ||||
| 20. Jornada | 28.03.2025 | FC Zlín | - | FC Sellier & Bellot Vlašim | 2:1 | ||||
| 21. Jornada | 06.04.2025 | Slavia Praha B | - | FC Zlín | 0:1 |  |
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| 22. Jornada | 11.04.2025 | FC Zlín | - | Zbrojovka Brno | 1:1 | ||||
| 23. Jornada | 16.04.2025 | Vysočina Jihlava | - | FC Zlín | 1:1 | ||||
| 24. Jornada | 20.04.2025 | FC Zlín | - | Baník Ostrava B | 1:1 |
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