Background There is increasing interest in promoting young people's health by modifying the school environment. However, existing research offers little guidance on how the school context enables or constrains students' health behaviours, or how students' backgrounds relate to these processes. For these reasons, this paper reports on a meta-ethnography of qualitative studies examining: through what processes does the school environment (social and physical) influence young people's health? Methods Systematic review of qualitative studies. Sixteen databases were searched, eliciting 62, 329 references which were screened, with included studies quality assessed, data extracted and synthesized using an adaptation of Noblit and Hare's meta-ethnographic approach. Results Nineteen qualitative studies were synthesised to explore processes through which school-level influences on young people's health might occur. Four over-arching meta-themes emerged across studies focused on a range of different health issues. First, aggressive behaviour and substance use are often a strong source of status and bonding at schools where students feel educationally marginalised or unsafe. Second, health-risk behaviours are concentrated in unsupervised 'hotspots' at the school. Third, positive relationships with teachers appear to be critical in promoting student wellbeing and limiting risk behaviour; however, certain aspects of schools' organisation and education policies constrain this, increasing the likelihood that students look for a sense of identity and social support via health-risk behaviours. Fourth, unhappiness at school can cause students to seek sources of 'escape', either by leaving school at lunchtime or for longer unauthorized spells or through substance use. These meta-themes resonate with Markham and Aveyard's theory of human functioning and school organisation, and we draw on these qualitative data to refine and extend this theory, in particular conceptualising more fully the role of young people's agency and student-led 'systems' in constituting school environments and generating health risks. Conclusion Institutional features which may shape student health behaviours such as lack of safety, poor student-staff relationships and lack of student voice are amenable to interventions and should be the subject of future investigation. Future qualitative research should focus on health behaviours which are under-theorised in this context such as physical activity, sexual and mental health.