Background: Education can create better opportunities for health, and vice versa. Using a so-called ‘add-in’ approach, school-based physical activity (PA) promotion and prevention of sedentary behaviours can increase pupils’ wellbeing and learning and, on the longer term, reduce the risk of non-communicable diseases. A PA ‘add-in’ approach involves integrating PA into teachers’ curricular obligations without being an extra burden as opposed to an ‘add-on’ approach which requires additional operational resources and include activities that do not explicitly contribute towards curricular targets making them less long-term acceptable in a school-based context. Previous studies investigating education outside the classroom (EOtC) show mutual benefits for both health and education outcomes among children and adolescents. However, the evidence is of mixed quality and questionable certainty, which calls for further investigation. The aim of this study protocol is to describe and discuss the study design and methods to investigate the efficacy and mechanisms of EOtC as a vehicle for health and education. The study investigates the intervention developed and conducted in the TEACHOUT study with updated and strengthened design and measures. Methods: The efficacy of EOtC will be investigated in a cluster randomised waitlist design. Participants will be pupils in ~54 classes, grades 4-10 (ages 10-15 years) in ~30 Danish elementary schools. Fifteen schools will be randomised to the intervention: a two-day EOtC training course targeting teachers followed by the teachers implementing EOtC >5 hours weekly over the course of one school year. Pre- and post-measures of health (PA and wellbeing) and learning (school motivation and academic achievement) will be collected. Investigation of pedagogical and motivational mechanisms will be based on observations of EOtC. Discussion: The updated randomised controlled design will provide firmer evidence for the efficacy and mechanisms of EOtC and provide knowledge about how mutual benefits of health and education can be obtained. Trial registration: Registered with ClinicalTrials.gov (ID NCT05237674) [University of Copenhagen. MOVEOUT: a Cluster RCT of the Efficacy, Mechanisms, and Mediation of an Education Outside the Classroom Intervention on Adolescents’ Physical Activity, 2023], February 14, 2022. Most recently updated on November 23, 2022 (Version 2).