Emotional and behavioral issues in adolescents pose significant obstacles to psychological well-being and academic achievement, potentially leading to severe mental health conditions. The escalating prevalence of these behavioral challenges can adversely affect a nation's educational, economic, and social health. This study aims to find appropriate solutions to behavioral problems and academic underperformance in adolescents through a two-arm randomized trial. It involves 200 students from distinct locations in India. Intervention encompasses integrated practices of yoga and physical exercises independently. Incorporation of ancient learning principles introduces a novel facet to the intervention protocol for educational and developmental purposes. Participants were evenly distributed across yoga and physical exercise groups. Preintervention and postintervention are evaluated through Strength and Difficulty Questionnaire alongside assessment of academic score of students. Findings exhibit a noteworthy transition among yoga group participants for behavioral problems from clinical risk status to normalized levels. Examination of the correlation between academic performance with various emotional and behavioral problems underscored the detrimental impact of these issues on scholastic attainment. Notably, the influence of yoga surpassed that of physical exercise in enhancing academic performance and mitigating emotional problems, conduct issues, hyperactivity, peer-related challenges, and overall strength and difficulty symptoms. The results suggest that the school-based interventions involving moderate to vigorous physical activity may be considered as a strategy to address adolescent mental health concerns and to enhance academic outcomes. It is further suggested that the policymakers and health professionals can explore such activities as an option to address the growing prevalence of mental health disorders.