Background: Participation in regular physical activity (PA) is important for both physical and mental health, and positive associations have also been reported between PA and academic performance. However, PA levels decline markedly during adolescence. School in motion (ScIM) is a school-based PA intervention carried out over one school year, in a sample of 14-year-old girls and boys. The primary aim was to investigate whether two extra hours of PA weekly lead to increases in the adolescents’ accelerometer assessed PA levels. Secondary aims were to investigate the intervention effects on time spent in PA of different intensities, muscle strength, cardiorespiratory fitness, mental health, academic performance and learning environment. ffigMethods & design: This is a multicenter, school-based, three-arm cluster randomized controlled trial (RCT) recruiting ninth graders from lower secondary schools in Norway. A total of 2084 14-year-olds from 29 schools were included, yielding a participation rate of 76 %. Schools (clusters) were randomly assigned to one of three study arms: (1) the physical active learning (PAL) intervention arm, (2) the don't worry-be happy (DWBH) intervention arm, or (3) current practice (control arm). All schools participating in ScIM had two or three mandatory PE-lessons per week. Schools in the two intervention arms added two hours of PA and PE to the class schedule each week. PA was assessed by accelerometers at baseline, midpoint and at the end of the intervention. All other variables were tested at baseline and at the end of the intervention. The measures included cardiorespiratory fitness, muscle strength, mental health (general mental health, quality of life and self-perception) academic performance (standardized national tests in reading and numeracy) and learning environment. Qualitative interviews were performed with students, teachers and school management to obtain an in-depth understanding of pedagogical processes taking place during the intervention.Discussion: This study will inform what effect two added hours of PA during the school week can have on adolescents’ PA levels, their health, academic performance and learning environment. Further, the study will add valuable information if the two PA interventions will generate different effects on important factors for learning and health.Trial registration: Clinicaltrials.gov ID nr: NCT03817047. Registered 01/25/2019 ‘retrospectively registered’