With the ongoing interest in implementing school policies to address the problem of childhood obesity in Malaysia, there is urgent need for information about the association between school environment and children's weight status. This study aims to investigate the association between school environmental factors (physical, economic, political and sociocultural) with BMI of school children in Terengganu. The school environment factors were assessed using a set of validated whole-school environmental mapping questionnaires, consisting of 76 criteria with four domains; physical environment (41 criteria), economic environment (nine criteria), political environment (nine criteria) and sociocultural environment (17 criteria). This involved face-to-face interview sessions with 32 teachers from 16 schools (eight rural and eight urban). In addition, 400 school children aged between 9 and 11 years of the selected schools were assessed for BMI (WHO 2007 reference chart), dietary intake (food frequency questionnaire (FFQ)) and physical activity level (physical activity questionnaire for children (PAQ-C)). Multiple regression was used to examine the association between school environment factors and BMI of the school children. Seven school environment criteria were found to be associated with BMI of school children when it was adjusted for calorie intake and physical activity level. About 33.4% of the variation in BMI of school children was explained by health professional involvement, simple exercise before class, encouragement to walk/ride bicycle to/from school, no high-calorie food sold, healthy options of foods and drinks at tuck shop, availability of policy on physical activity and training teacher as a role model. Policy makers should make urgent actions to address the obesogenic features of school environments. It should strive towards setting up healthy school environment and improving school curricula to promote healthy behaviours among the school children.