Background and Aim: Functional Movement Screening (FMS) which plays an important role in predicting sports injuries, has been recommended by many sports experts in designing exercise programs. The present study aimed to evaluate the effects of functional movement training program on functional movement screening scores and selected physical fitness factors in active military men. Methods: Thirty eight active injury-prone military men were divided into experimental (n=18) and control (n=20) groups based on functional movement screening and without any injury using the convenience and purposive method. Functional movement Screening (FMS) was evaluated by a set of FMS and flexibility tests through sit and Reach test; Dynamic Balance was evaluated by Y-Balance Test (YBT); and the explosive power by the Sargent's jump test. The experimental group performed the functional movement training program for eight weeks. Results: The comparison of total FMS score indicated a significant difference (P<0. 05 and effect size=0. 64) between experimental and control groups. There was also a significant improvement in the scores of flexibility (p<0. 05 and effect size=0. 87), dynamic balance (p<0. 05 and effect size=0. 78) and explosive power (p<0. 05 and effect size=0. 68). Conclusion: According to results, the functional movement training program could increase scores of functional movement screening and physical fitness in active military men. Therefore, it seems that this training program can reduce the risk of injury in injury-prone individuals.