Introduction The home and school environments play important roles in influencing children’s health behaviours. However, their simultaneous influence on childhood obesity has not yet been examined. We explore the relationship of the home and school environments with childhood obesity, to determine whether this relationship is mediated by children’s fruit and vegetable intake and physical behaviours. Methods This study uses baseline data from 9 to 11 year old children, their parents and school principals (matched data n = 2466) from the Obesity Prevention and Lifestyle Project. Child-reported behaviours, parent-reported home environment and principal-reported school environment data were collected via questionnaires. Trained researchers measured children’s height and weight, and Body Mass Index (BMI, kg/m 2 ) was calculated. Structural equation modelling was used to assess the relationship of the home and school environments with children’s fruit and vegetable intake, physical activity behaviours, and children’s BMI. Result The home diet environment was positively associated with child diet (β = 0.18, p < 0.001). The home physical activity environment had the largest inverse association with BMI (β = − 0.11, p < 0.001), indirectly through child physical activity (β = 0.28 ,p < 0.001). Schools’ healthy eating policy implementation was significantly associated with child diet (β = 0.52, p < 0.05), but physical activity policy was not associated with child activity (β = − 0.007, p > 0.05). The school environment was not associated with child BMI. Discussion The home environment had a stronger association with healthier child behaviours, compared to the school environment. These findings suggest that future childhood obesity interventions targeting healthier home environments and supporting parents can promote healthier child eating and physical activity behaviours.