Introduction: Appropriate movement patterns are important for both injury prevention and athletic performance. Therefore, the use of Functional Movement Screen (FMS), which has been shown to be effective in predicting sport injuries, is recommended by many sports specialists in designing training programs. On the other hand, questions remain regarding its utility as a means to evaluate the effectiveness of training. The purpose of the present study was to investigate whether a functional training program can affect the fundamental movement patterns.Materials and Methods: The study participants consisted of 27 youth male soccer players in the age range of 14 to 16 years and free from pain and previous injury in different layers. The subjects were allocated to experimental and control groups. The experimental group performed functional training for 10 weeks. The total time devoted to training was the same in both groups. Before and after the functional training, FMS was evaluated in both groups. Independent t-test and ANCOVA were used for statistical analysis at the significance level of P < 0.05.Results: A significant difference was observed in FMS score between experimental group (18.07 ± 1.49) and control group (16.07 ± 1.11) (P < 0.001; Effect size = 0.71).Conclusion: This study demonstrated that fundamental movement patterns improved as a result of a functional training intervention in youth male soccer players. Therefore, coaches and sports specialists can be recommended to pay special attention to functional training. The investigation of the effect of functional training on other injury risk factors in future studies seems necessary.