This study examined the association between functional movement (FM) and adiposity in adolescent population (16–17 years). This study was conducted in a representative sample of urban adolescents as the part of the CRO-PALS longitudinal study (n = 652). Body mass index (BMI), a sum of four skinfolds (S4S), waist and hip circumference were measured, and FM was assessed via Functional Movement ScreenTM (FMSTM). Furthermore, total FMSTM screen was indicator of FM with the composite score ranged from 7 to 21, with higher score indicating better FM. Multilevel analysis was employed to determine the relationship between different predictors and total FMS score. In boys, after controlling for age, moderate-to-vigorous physical activity, and socioeconomic status, total FMS score was inversely associated only with BMI (β = −0.18, p < 0.0001), S4S (β = −0.04, p < 0.0001), waist circumference (β = −0.08, p < 0.0001), and hip circumference (β = −0.09, p < 0.0001). However, among girls, in adjusted models, total FMS score was inversely associated with S4S (β = −0.03, p < 0.0001), while BMI (β = −0.05, p = 0.23), waist circumference (β = −0.04, p = 0.06), and hip circumference: (β = −0.01, p = 0.70) failed to reach statistical significance. Results showed that the association between adiposity and FM in adolescence is sex-specific, suggesting that boys with overweight and obesity could be more prone to develop dysfunctional movement patterns. Therefore, exercise interventions directed toward correcting dysfunctional movement patterns should be sex-specific, targeting more boys with overweight and obesity rather than adolescent girls with excess weight.