Background: Schools are a key setting for health promotion and improvement activities and the psycho-social environment of the school is an important dimension for promoting the health and well-being of children. The development of Health Promoting Schools (HPS) draws on the settings-based approach to health promotion and includes child participation as one of its basic values. This paper investigates the relationships between child participation, the school environment and child outcomes.Methods: Study participants were recruited from nine primary schools, three of which were designated as Health Promoting Schools (HPS). Each HPS was matched with two non-HPS (NHPS) with similar characteristics. Two hundred and thirty-one pupils in the 4th-6th class groups completed self-report questionnaires to document their perspectives on the school socio-ecological environment, how they take part in school life, school processes and their health and well-being.Results: School participation was measured with four scales: participation in school decisions and rules, school activities, school events and positive perception of school participation. The differences in the reported mean score for three of the four scales were marginal and not statistically significant. However, the mean score for reported positive perception of school participation was significantly lower (X-2 = 5.13, df = 1, p < 0.05) among pupils in HPS (mean = 26.03; SD 3.37) compared to NHPS (mean = 26.30; SD 3.36). Participation in school decisions and rules (OR 1.22, 95% CI 1.12-1.33), participating in school activities (OR 1.20, 95% CI 1.10-1.31), participating in school events (OR 1.19, 95% CI 1.10-1.29) and reported positive perception of school participation (OR 1.26, 95% CI 1.15-1.39) were all positively associated with health and well-being outcomes for all pupils. Logistic regression analyses indicated positive associations between school participation and school socio-ecological environment.Conclusions: These findings suggest that school participation is important for children in schools and is relevant for improved school environment, relationships and positive health and well-being outcomes. The positive associations between school participation and school socio-ecological environment and health and well-being outcomes suggests that pupil health and well-being and school relationships could be improved or sustained by providing or supporting an environment that encourages pupil participation in school life.