Indonesia is currently facing double burden malnutrition in children. As overweight and obesity are due to a disturbed energy balance, this study aimed to assess the association of total energy intake and physical activity with the prevalence of overweight among Indonesian children.The data used for this analysis were from 1143 children, 6-12 years old, that participated in the South East Asian Nutrition Survey (SEANUTS). Physical activity (PA) was measured using pedometers for 2 consecutive days and was categorized low, moderate and high. Child nutritional status was categorized based on body mass index for age z-scores (BAZ) into normal weight (-2 SD ≤BAZ≤1 SD) or overweight (BAZ >1 SD). Energy intake was calculated from a one day 24 hour recall and compared to the Indonesian recommended dietary allowance (RDA) for energy.Children with low PA had higher risk (ODDs 3.4, 95% CI: 2.0, 6.0) of being overweight compared to children who had high PA. Children with moderate PA and energy take >100% RDA had higher risk (ODDs 4.2, 95% CI 1.9, 9.3) of being overweight than children with high PA and energy intakes ≤100% RDA.Low physical activity independently or moderate physical activity and high energy intake are risk factors for Indonesian children to get overweight. Program intervention such as increasing physical activity at school and home is needed to reduce overweight among children.