Objective To assess the feasibility, acceptability, and potential efficacy of a school-based obesity prevention program among adolescent boys with sub-optimal cardiorespiratory fitness. Methods In 2007, a 6-month, 2-arm parallel group, randomized controlled pilot trial was conducted in a single school setting (Sydney, Australia). Thirty-three 7th Grade boys (mean age = 12.5 ± 0.4 years) were randomly assigned to intervention ( n = 16) or active comparison group ( n = 17). The intervention consisted of one 60-minute curriculum session and two 20-minute lunchtime physical activity sessions per week. The active comparison group continued with their usual physical activity curriculum sessions (Friday afternoons 2–3 pm). The pilot trial's curriculum sessions were additional to Physical Education (PE) lessons. The primary outcome was BMI, and secondary outcomes included waist circumference, percentage body fat, cardiorespiratory fitness, objectively measured physical activity and small screen recreation time. Results Screening, recruitment and retention goals were exceeded. The majority of data were collected as planned. Implementation and attendance rates were acceptable. At follow-up, compared with boys in the active comparison group, boys in the intervention group displayed a smaller increase in BMI (adjust diff. = − 0.2, 95% confidence interval [CI] − 0.78, 0.39; Cohen's d = 0.05); greater reductions in waist circumference (− 1.65 cm [− 4.67, 1.36]; d = 0.15); percentage body fat (− 1.69% [− 4.98, 1.60]; d = 0.22) and time spent in small screen recreation on weekends (− 1.13 h [− 5.06, 2.80]; d = 0.19); and a greater increase in cardiorespiratory fitness (2.13 laps [6.22, 10.48]; d = 0.16); and participation in total weekday physical activity (140.74 counts/min [− 159.44, 440.92]; d = 0.36). Conclusions This study verified the feasibility, acceptability and potential efficacy of a multifaceted school-based intervention to prevent unhealthy weight gain among adolescent boys.