Background <p>Physical fitness is a powerful marker of current and future health in children and adolescents. However, global reports have long documented a persistent decline, with an even greater decline among girls. This study aimed to examine the impact of school-based resistance training (RT) on physical fitness and body composition in pubertal girls.</p> Methods <p>A randomized controlled trial was conducted over eight weeks, with sessions held three times a week. RT program was conducted during physical education classes. A total of 79 girls from four schools were randomly assigned to one of four groups: control group (CON, <i>n</i> = 21), traditional strength training group (TST, <i>n</i> = 20), plyometric training group (PT, <i>n</i> = 19), and combined training group (CT, <i>n</i> = 19). Pre- and post-intervention assessments were performed by evaluating body composition, musculoskeletal fitness, cardiorespiratory fitness, speed and agility.</p> Results <p>Significant improvements were observed in TST for push-ups, 1&#xa0;min sit-ups, standing long jump (SLJ) and 50&#xa0;m sprint (<i>p</i> &lt; 0.05). PT and CT groups displayed valuable improvement in push-ups, SLJ, 50&#xa0;m sprint and Illinois changes of direction test (<i>p</i> &lt; 0.05). Notably, CT yielded a significant increase in the 20&#xa0;m shuttle run test (<i>p</i> &lt; 0.001). However, non-significant changes in body composition were observed across intervention groups.</p> Conclusion <p>RT program implemented during physical education classes was effective in improving physical fitness. Each RT modalities offering unique advantages.</p> Clinical trial number <p>ChiCTR2500103789; Retrospectively registered on 5/6/2025.</p>