OBJECTIVES: This study examined the relationship between functional movement and physical activity (PA) levels in adolescents. DESIGN: Cross-sectional study. SETTING: This research is a part of the CRO-PALS longitudinal study conducted in a random sample of adolescents in Zagreb at the Faculty of Kinesiology, University of Zagreb, Croatia. PARTICIPANTS: Seven hundred and twenty-five adolescents aged between 16 and 17 years were included. MAIN OUTCOME MEASURE: Total Functional Movement Screen score (total FMS score). RESULTS: After adjusting for age, body fat and SES, both VPA and MVPA showed minor but significant effects on total FMS score among girls (β = 0.011, p = 0.001, β = 0.005, p = 0.006, respectively), but not in boys (β = 0.004, p = 0.158; β = 0.000, p = 0.780). Regarding PA type, volleyball and dance improved total FMS score (β = 1.003, p = 0.071; β = 0.972, p = 0.043, respectively), while football was associated with lower FMS score (β = -0.569, p = 0.118). CONCLUSION: Results suggest that the PA level is positively associated with the functional movement in adolescent girls, but not in boys, where the type of PA moderates these associations. Therefore, functional movement patterns incorporated into physical education curriculum could be beneficial to the musculoskeletal health of the children.