| 16. Round | 08/03/2025 | FK Mladá Boleslav [Youth B] | - | 1. FC Slovácko [Youth B] | 1:4 |  |
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| 17. Round | 14/03/2025 | FC Zlín [Youth B] | - | FK Mladá Boleslav [Youth B] | 2:2 | ||||
| 18. Round | 22/03/2025 | FK Mladá Boleslav [Youth B] | - | Sigma Olomouc [Youth B] | 1:3 | ||||
| 19. Round | 28/03/2025 | FC Zbrojovka Brno [Youth B] | - | FK Mladá Boleslav [Youth B] | 2:2 | |
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| 20. Round | 05/04/2025 | FK Mladá Boleslav [Youth B] | - | Banik Ostrava [Youth B] | 3:0 | |
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| 21. Round | 12/04/2025 | Dynamo České Budějovice [Youth B] | - | FK Mladá Boleslav [Youth B] | 1:1 | ||||
| 26. Round | 17/05/2025 | FK Pardubice [Youth B] | - | FK Mladá Boleslav [Youth B] | 3:2 | ||||
| 27. Round | 24/05/2025 | FK Mladá Boleslav [Youth B] | - | Slavia Praha [Youth B] | 2:1 |
Czech Republic