Background: Young people spend a large proportion of their time in school, which presents both risk and protective factors for their mental health. A supportive school culture can promote and protect good mental health by creating experiences of safety and belonging amongst staff and students. In this qualitative study, we seek to explore whether a participatory action research (PAR) approach is an effective way to promote and improve student mental health. Methods: Participatory action research is an approach in which people collaboratively research their own experience: the researched communities become co-researchers of their own experiences in a specific context. We will work with four secondary schools in the UK to develop PAR projects. In each school, a group of 2–4 staff and 6–8 students will work together to develop a shared understanding of their school culture and to introduce activities or changes to make the culture more supportive of student mental health. We will evaluate the effectiveness of the PAR approach through i) a review of school documents pertaining to mental health (e.g., policies and Ofsted reports), ii) interviews with staff members (n = 40), parents (n = 8) and students (n = 24–40) before and after the PAR intervention, iii) observations and reports of the PAR group meetings and iv) interviews with members of the PAR groups after the PAR intervention. Discussion: We anticipate that our research findings will advance knowledge on effective methods to develop a positive school culture that will contribute to the improvement of young people’s mental health and well-being. We will seek to identify the mechanisms through which school culture can have a positive impact on mental health and develop a logic model and a school culture toolkit that can be utilised as a resource to inform public health interventions to promote mental health in a range of educational settings.