BACKGROUND: Regular participation in moderate-to-vigorous physical activity (MVPA) is important to manage obesity. Physical education (PE) is considered to play an important role in promoting lifelong participation in physical activity (PA) because it provides an existing network where cost-effective interventions can be implemented to produce sustainable change in health behavior. However, the association between compulsory school PA (e.g., PE lessons) and body composition levels has received mixed support in the literature. Therefore, the present study aimed to investigate whether a school-based intervention targeting salient PA benefits and barriers grounded on the theory of planned behavior would promote young people's participation in MVPA during leisure time and reduce body mass index (BMI) of overweight students. METHODS/DESIGN: A total of 171 students from 3 secondary schools in Singapore underwent the control condition followed by the intervention condition. Both the conditions consisted of PE lessons twice per week over 4 weeks. In the control condition, PE teachers encouraged students to participate in PA during leisure time without providing persuasive message. While in the intervention condition, PE teachers delivered persuasive messages that targeted the salient benefits and barriers associated with PA to the students at the last 5 to 10 min of each PE lesson. PA levels over a week were measured objectively with wrist-mounted GENEActiv Original accelerometers and subjectively with self-reporting questionnaires three times (Baseline, Post 1, and Post 2) in each condition. Student's self-reported PA level was measured using the Leisure-Time Physical Activity Participation Questionnaire and the International Physical Activity Questionnaire, and their attitudes, intentions, subjective norms and perceived behavior control towards leisure-time PA were measured with a questionnaire based on the theory of planned behavior. Furthermore, students' intention, determination and willingness to engage in leisure-time PA were compared with the other activity (e.g., doing homework, shopping). DISCUSSION: This study will provide the evidence on the effectiveness of a cost-effective school-based intervention on reducing BMI of overweight students through promoting sustained participation in leisure-time PA. It will also address methodological issues on the gaps between objective and subjective measures of PA. TRIAL REGISTRATION: This trial is registered with the ISRCTN registry (ISRCTN73786157, 26/10/2017, retrospectively registered).