INTRODUCTION: Despite the known health and educational benefits of physical activity and the risks of prolonged sedentary behaviour, only one in 10 adolescents globally meet physical activity guidelines, and three-quarters of the school day is spent sitting. METHODS AND ANALYSIS: A type II hybrid implementation-effectiveness trial will be conducted using a mixed-methods design. For the implementation trial, ETHICS AND DISSEMINATION: These trials were approved by the Deakin University Human Research Ethics Committee (2021-269) and by the following education authorities: Australian Capital Territory Education Directorate (RES 2317), New South Wales Department of Education (2022253), Northern Territory Department of Education (20865), Victoria Department of Education (2023_004712), Queensland Department of Education (550/27/2585), South Australian Department of Education (2022-0019), Tasmanian Department of Education (2022-25), Western Australian Department of Education (D23/1152724), and Melbourne Archdiocese Catholic Schools (1232). Results from this study will be disseminated through peer-reviewed journal articles, scientific conferences, summary reports to students and schools and stakeholder meetings. TRIAL REGISTRATION NUMBER: Australian Clinical Trials Registration Registry (ACTRN12622000600741).