Schools offer a valuable setting to promote good health and mental well-being amongst young people. Schools are complex systems and therefore systems interventions are needed to improve pupil health and well-being. This paper presents a qualitative process evaluation of the South West- School Health Research Network, a systems level intervention. The evaluation is based on interviews with school staff, local authorities and wider stakeholders. Given the complexity of England's educational system there is a need to intervene and monitor health at multiple levels and to ensure close partnership working to effectively improve adolescent health through schools.