Evidence that health and education are interlinked is transforming investment in adolescent health. However, no comprehensive theory of how schools influence mental and physical health, which could guide, and be tested through, empirical studies, exists. Using neuroscience, sociology, and other disciplines, we theorise that schools catering for students age 11-18 years can influence health by affecting the behavioural roles that are available for students to perform, the resources available to influence student behaviour, and how peers and teachers (known as the audience) respond. Some schools offer opportunities for students to adopt diverse pro-school roles and to maintain these roles via constructive feedback. Other schools focus narrowly on high academic attainment. Where pro-school roles are unavailable, are beyond students' resources, or elicit negative responses from teachers and peers, students might experience anxiety and choose to adopt anti-school roles, particularly in later adolescence. Behaviours that harm health, such as violence and drug use, are central to anti-school roles because they can facilitate belonging and status within anti-school peer groups and symbolise alternative transitions to adulthood.