| 8. Round | 01/09/2024 | Zbrojovka Brno | - | FC Zlín | 1:2 | ||||
| 10. Round | 22/09/2024 | Baník Ostrava B | - | FC Zlín | 0:1 | ||||
| 14. Round | 26/10/2024 | MFK Vyškov | - | FC Zlín | 1:1 | ||||
| 15. Round | 04/11/2024 | FC Zlín | - | MFK Chrudim | 2:0 | ||||
| 16. Round | 09/11/2024 | FK MAS Táborsko | - | FC Zlín | 0:0 | ||||
| 17. Round | 03/03/2025 | FC Zlín | - | 1. SK Prostějov | 3:0 | ||||
| 18. Round | 09/03/2025 | Sigma Olomouc B | - | FC Zlín | 1:2 | ||||
| 19. Round | 16/03/2025 | Viktoria Žižkov | - | FC Zlín | 1:3 | ||||
| 20. Round | 28/03/2025 | FC Zlín | - | FC Sellier & Bellot Vlašim | 2:1 | ||||
| 21. Round | 06/04/2025 | Slavia Praha B | - | FC Zlín | 0:1 |  |
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| 22. Round | 11/04/2025 | FC Zlín | - | Zbrojovka Brno | 1:1 | ||||
| 23. Round | 16/04/2025 | Vysočina Jihlava | - | FC Zlín | 1:1 | ||||
| 24. Round | 20/04/2025 | FC Zlín | - | Baník Ostrava B | 1:1 | ||||
| 25. Round | 27/04/2025 | AC Sparta Praha B | - | FC Zlín | 1:0 | ||||
| 26. Round | 02/05/2025 | FC Zlín | - | FK Varnsdorf | 2:0 | ||||
| 27. Round | 07/05/2025 | SFC Opava | - | FC Zlín | 0:1 |  |
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| 28. Round | 11/05/2025 | FC Zlín | - | MFK Vyškov | 2:1 | ||||
| 29. Round | 17/05/2025 | MFK Chrudim | - | FC Zlín | 0:0 |
Czech Republic