Children aged 10-11 years pass through a dynamic developmental period marked by rapid changes in body size, shape, and composition, all of which are sexually dimorphic. The purpose of this study was to analyze the effects of gender on a school-based intervention in the prepubertal growth spurt. One hundred twenty-five healthy children (58 boys, 67 girls), fifth and sixth grade students from an urban public elementary school in Portugal (10.8 ± 0.4 years), were randomly assigned into two experimental groups: a strength training group (19 boys, 22 girls), and an endurance training group (21 boys, 24 girls); and a control group (18 boys, 21 girls; no training program). Training program for the two experimental groups was conducted twice a week for 8 weeks. Compared with the values at the beginning of the protocol, both strength and endurance training programs produced significant improvements (p< 0.05) in vertical and horizontal jumps, a 1 kg and 3 kg medicine ball throw, a 20 m sprint and VO2max, for both boys and girls. No significant changes were observed related to gender in training-induced strength (p> 0.05, ƞ_p^2= 0.16, Power= 0.29) and aerobic (p> 0.05, ƞ_p^2= 0.05, Power= 0.28) capacity. The results of the present study should be taken into consideration in order to optimize strength training school-based programs.