Background Overweight youths are generally recognised as being at increased risk of sustaining lower extremity injuries in sports. However, previous studies are inconclusive and choices for measuring overweight are manifold. Objective To examine two different measures of overweight, body mass index (BMI) and total body fat percentage (TBF%), as risk factors for lower limb injuries in a school-based cohort. Study design A longitudinal cohort study. Methods A total of 632 school children, baseline age 7.7-12.0 years, were investigated. Whole body dual energy x-ray absorptiometry scans provided measures of TBF%. Measures of BMI were obtained by standard anthropometric methods. Musculoskeletal complaints were reported by parents answering weekly mobile phone text messages during 2.5 years. Injuries were diagnosed by clinicians. Leisure time sports participation was reported weekly using text messaging. Results During 2.5 years of follow-up, 673 lower extremity injuries were diagnosed. Children being overweight by both BMI and TBF% showed the highest risk of sustaining lower extremity injuries (IRR 1.38 (95% CI 1.05 to 1.81)). Children who were overweight using BMI and TBF% showed the highest risk of sustaining lower extremity injuries (IRR 1.38 (95% CI 1.05 to 1.81)). Conclusions The risk of lower extremity injuries appeared to be increased for overweight children. When comparing two different measures of overweight, overweight by TBF% is a higher risk factor than overweight by BMI. This suggests that a high proportion of adiposity is more predictive of lower extremity injuries, possibly due to a lower proportion of lean muscle mass.