Health outcomes vary between schools and it is theorised that this may be partly attributable to variation in the school environment. Existing systematic reviews have not drawn authoritative conclusions because of methodological limitations in the review or studies available. We identified 42 multi-level studies, ten of which were judged of sufficient quality to narratively synthesize. There was consistent evidence that schools with higher attainment and attendance than would be expected from student intake had lower rates of substance use. Findings on the influence of smoking/alcohol policies were mixed. Three studies examined the health effects variously associated with school campus area and observability, year structure, school size and pupil-to-teacher ratio with mixed findings. The studies reviewed support the potential influence of the school environment on student health.