The functional movement screen (FMS) is commonly used to assess movement capacity and determine injury risk. Evidence suggests that athletes who score 14 points or less on the FMS are at increased risk for injury, but differences between males and females have been minimally studied. The purpose of this study was to investigate sex differences in FMS scores of secondary school athletes. Using a cross-sectional study design, 60 healthy secondary school athletes performed the FMS, which is composed of 7 functional movement tasks (deep squat, hurdle step, inline lunge, shoulder mobility, active straight-leg raise, trunk stability push-up, and rotary stability) and 3 clearance screens. Dependent variables were FMS total composite score and individual task scores; secondary analyses were performed using total research score and individual task research scores when indicated. Lower scores indicated functional movement deficits and increased injury risk. Healthy secondary school female athletes scored lower on the total composite (p = 0.004) than healthy secondary school male athletes. Females also scored lower on the following individual FMS tasks: inline lunge (p < 0.04) and trunk stability push-up (p = 0.001). Healthy secondary school female athletes scored 14 or less on the FMS total composite score and significantly lower in general compared with healthy secondary school male athletes, which suggests these female athletes may be at higher risk for injury. Factors that may contribute to increased injury risk include deficits in mobility, core stabilization, and coordinated movement patterns. Clinicians should be aware of possible sex differences when using the FMS and developing injury prevention programs.