BACKGROUND: In recent decades, physical activity intervention programs have been developed to reduce overweight and obesity in adolescents. However, this population is considered hard to reach in physical activity programs due to lack of adherence and poor results. Interventions with mobile phones in the adolescent population with normal weight have shown benefits, so this line of research may provide benefits in adolescents with overweight or obesity, although it has not yet been explored in the scientific literature. OBJECTIVE: This study aims to determine the changes produced by a 10-week intervention promoted during school lessons on physical education using step tracker mobile apps in out-of-school hours on physical activity, adherence to the Mediterranean diet, body composition, and the physical condition of adolescents who are overweight and obese, and to analyze the changes achieved by the 10-week intervention on the psychological state of adolescents who are overweight and obese. METHODS: The study was based on a randomized controlled trial with an initial sample of 50 adolescents aged between 12 and 16 years (from the first to the fourth years of compulsory secondary education), whose body composition, physical activity level, physical condition, and psychological state were measured. Participants were divided into an experimental group (EG) and a control group (CG), where the EG performed a series of walking steps with a mobile app in their free time outside physical education classes. Adolescents in the CG continued to perform their physical activities as normal but did not use any mobile apps. Inclusion in the EG and CG was randomized, and the researchers were blinded. RESULTS: An increase was found in the EG in corrected arm girth (mean difference -0.46; P=.05), curl-up repetitions (mean difference -6.35; P=.02) and push-up repetitions (mean difference -2.27; P=.04) after the intervention. In the CG, there was a significant increase in hip girth (mean difference -1.37; P=.05), corrected thigh girth (mean difference -1.28; P=.04), and muscle mass (mean difference -0.87; P=.04), as well as a significant decrease in competence (mean difference 3.08; P=.03). The covariates gender and age showed an effect on corrected arm girth (gender: P=.04), curl-up repetitions (gender: P=.04) and push-up repetitions (gender: P=.04) in the EG; while in the CG it affected corrected thigh girth (gender: P=.04), adherence to the Mediterranean diet (gender: P=.04 and age: P=.047) competence (gender: P=.04 and age: P=.04) and relatedness (gender: P=.05 and age: P=.04). No significant differences were found when comparing changes in the CG and EG. CONCLUSIONS: A 10-week program of mobile app use by adolescents who are overweight and obese for physical activity outside of school hours does not appear effective in producing improvements in body composition, physical fitness, or adequate psychological state as it does not appear to significantly increase physical activity. TRIAL REGISTRATION: ClinicalTrials.gov NCT06089876; http://clinicaltrials.gov/ct2/show/NCT06089876.