School has a significant role in providing opportunities for children to engage in physical activity (PA) through policies and practices. This study aimed to identify the prevalence of school policies and practices related to physical activity (PA) and their association with Thai students' overall and domain specific PA. This cross-sectional analysis included 5,830 students aged 6-17 years from 136 schools recruited though a multi-stage stratified cluster sampling across Thailand. Student's PA data were assessed using a student survey and school data were collected by a principal survey. Associations between students' PA and school variables were examined using logistic regressions. Despite a high prevalence of Thai schools reporting many policies and practices promoting PA in different areas, students reported low levels of PA. None of the school PA policies and practices was associated with students' overall and domain specific activities, with active transport as the one exception. When schools had an active transport policy, students were 40% (OR = 1.40, p = 0.01) more likely to travel actively to/from school. The identified positive relationship between school active transport policy and students' active travel behavior suggests a potential wider adoption of the policy promoting school active transport aiming to increase student's PA levels among all Thai schools. Intervention studies are necessary to confirm this finding. Our study also reflected that, for greater levels of children's school-based PA, strategies to translate the existing school PA policies into effective implementation should be an emphasis for Thai schools.