AbstractSchools are important social institutions which play a role in reducing and amplifying inequalities, including health inequalities. A growing evidence base indicates that school and family socioeconomic status (SES) interact to create positive and negative health outcomes, with ‘benefits’ of attending a higher SES school greatest for children from higher SES families. School connectedness is an increasingly studied mechanism, or set of mechanisms, for improving health and reducing health inequalities. Studies on interactions of school and family SES and on school connectedness have to date focused mainly on secondary schools. This paper presents multilevel analyses of survey data from 17,000 primary school children in Wales, aged 9–11 years. It finds that school and family SES are independently associated with health behaviours and mental health and wellbeing outcomes, and interact, with ‘benefits’ of attending a higher SES school greatest for children from higher SES families. Exceptions include some risk behaviours, most common among children from higher SES families in lower SES schools. School connectedness was associated with most outcomes, with some variations between components of school connectedness. Interactions were consistent with greater benefit of attending a higher SES school for children from higher SES families in relation to peer environment, but not for other aspects of school connectedness. Better understanding mechanisms via which family SES may be amplified or attenuated by school characteristics is vital in informing intervention to reduce health inequalities. This paper provides some evidence that school connectedness may be an important target mechanism for interventions to improve health and reduce inequalities.