The purpose of this study was to investigate the physiological adaptations of resistance training (RT) in prepubertal boys. Eighteen healthy boys were divided into RT (n = 9, M_age = 10.4 ± 0.5 years) and control (CTR; n = 9, M_age = 10.9 ± 0.7 years) groups. The RT group underwent a resistance training during 12 weeks, 3 times per week, performing 3 sets of 6 to 15 repetitions at intensities ranging from 60% to 80% of maximal dynamic strength (1-repetition maximum [1-RM] values). Before and after the training, the groups were assessed in their body mass and composition (dual-energy X-ray absorptiometry), isokinetic dynamometry, 1-RM, and ergoespirometry. Moreover, force per unit of muscle volume was calculated by the quotient between 1-RM and lean mass. Both groups presented statistically significant (p < .05) increases in the 1-RM and force per unit of muscle volume in the knee extension and elbow flexion, but these strength increases were statistically significantly greater in the RT group (effect size [ES] = 2.83–9.00) than in the CTR group (ES = 0.72–1.00). Moreover, both groups statistically significantly increased in lean body mass variables (ES = 0.12–0.38). However, increases in the fat mass variables occurred only in the CTR group (ES = − 0.01–0.50), whereas no changes were observed in the RT group. Furthermore, there were statistically significant increases in all bone mineral content variables (ES = 0.13–0.43), without differences between groups. No cardiorespiratory changes were observed. Twelve weeks of RT was effective in improving strength and force per unit of muscle volume and prevented fat mass increases in boys.