Adolescents spend the majority of the day sedentary, especially at school whilst sitting in class and at home when following lessons online or performing school-related tasks. As high levels of sedentary time are associated with adverse physical and mental health effects and lower cognitive performance in youth, effective interventions are needed. To improve effectiveness, literature recommends a participatory approach in which adolescents are actively involved in the choice and development of intervention strategies. Therefore, this project aims to develop and implement a participatory intervention to target adolescents’ sedentary behaviour at school and at home for school-related activities using the systematic approach of the Intervention Mapping Protocol. Further, the added effect of a participatory approach on adolescent’s mental wellbeing, cognitive performance, sedentary behaviour and related determinants will be evaluated via a three-arm clustered randomized controlled trial, including a participatory intervention arm, a standard intervention arm and a control arm. Lastly, we will conduct a process evaluation of (1) the participatory approach used to develop, implement and evaluate the intervention and (2) the intervention itself. Studies that evaluate interventions, developed with a participatory approach, are scarce. However, if such interventions prove to be more effective, this approach could be promising to change adolescents' health behaviour.