| 16. Round | 08/03/2025 | Vysočina Jihlava [Youth B] | - | FC Zlín [Youth B] | 6:3 |  |
|||
| 17. Round | 14/03/2025 | FC Zlín [Youth B] | - | FK Mladá Boleslav [Youth B] | 2:2 | ||||
| 19. Round | 29/03/2025 | FC Zlín [Youth B] | - | Slavia Praha [Youth B] | 3:7 | ||||
| 20. Round | 05/04/2025 | FK Jablonec [Youth B] | - | FC Zlín [Youth B] | 1:2 | ||||
| 21. Round | 12/04/2025 | FC Zlín [Youth B] | - | Slovan Liberec [Youth B] | 0:0 | ||||
| 22. Round | 18/04/2025 | SFC Opava [Youth B] | - | FC Zlín [Youth B] | 0:1 | |
 |
||
| 23. Round | 26/04/2025 | FC Zlín [Youth B] | - | 1. FC Slovácko [Youth B] | 2:3 | ||||
| 24. Round | 03/05/2025 | AC Sparta Praha [Youth B] | - | FC Zlín [Youth B] | 3:1 | ||||
| 25. Round | 10/05/2025 | Sigma Olomouc [Youth B] | - | FC Zlín [Youth B] | 7:0 | ||||
| 26. Round | 17/05/2025 | FC Zlín [Youth B] | - | FC Zbrojovka Brno [Youth B] | 1:2 |
Czech Republic