Physical education is a favourable educational framework for the development of programmes aimed at increasing physical activity in children and thus reducing sedentarism. The progressive increase of overweight students demands global control and follow-up measurement of these behaviours in both in and out of school. The pedometer can be a useful tool in this field. It is easy to use and allow Physical Education (PE) departments to quantify their students' number of steps/day. The aim of this study was to determine the effect of a pedometer intervention on body fat and BMI levels in overweight teenagers. Besides, the effects of the programme are analysed according to two other variables: pedometer ownership and gender, distinguishing between out-of-school and school hours, weekdays and weekends. The sample comprises 112 overweight students (49 boys and 63 girls) from 5 secondary schools. Participants were asked to follow a physical activity programme consisting on a minimum of 12000 and 10000 steps/day for boys and girls, respectively. It also allowed them to get up to 2 extra points in their PE marks. Results were measured after 6 weeks of programme application as well as after 6 weeks of retention. Results revealed significantly reduced BMI in the teenagers with their own pedometer (p < 0.05). The difference observed in the number of steps/day between boys (12050) and girls (9566) was significant in all measured time periods (p < 0.05). Besides, both overweight boys and girls were observed to take 1000 steps/day less at weekends than in weekdays. Therefore, it is concluded that the proposal of 12000 and 10000 steps for overweight boys and girls, respectively, accompanied by a reinforcement programme in their final PE marks, seems sufficient to obtain significant BMI reductions. Besides, PE is shown a favourable framework for the proposal of pedometer-impelled weight loss programmes in overweight youth.