Prevalence of overweight and obesity is an important health problem worldwide. It was shown that physical activity and sedentary behaviour are associated with prevalence of overweight and obesity in youth individuals. However, few children and adolescents meet the World Health Organization recommendations about physical activity levels. The need to start promoting regular physical activity from an early age is crucial to avoid these problems. Therefore, the aim of the current research is to show a school-based motivational program for the promotion of healthy lifestyle in inactive adolescents grounded on Self-Determination Theory aimed at promoting physical activity adherence. The study is a quasi-experimental study (ClinicalTrials.gov ID: NCT03974607) aimed for adolescents from the 1st and 2nd high school level aged between 12 and 14 years old. The program will be based on the promotion of the three basics psychological needs: autonomy, competence and relatedness. The satisfaction of these needs is essential to fulfill the self-determined motivation and psychological well-being. The length of the sessions are 60 min, 3 times per week, during 5 months. The sessions will be based on the participants’ interests. Finally, this protocol will intend to change the perception of physical activity programs in order to focus the strategies on the motivational aspects, rather than physical activity itself as was usually conducted by previous programs