Introduction:The increasing prevalence of childhood obesity among primary school children is a growing public health concern worldwide. Previous study in West Malaysia showed a prevalence of obesity with an estimated of 6.6% among 7-year-olds children and rising to 13.8% among 10-year-olds children. However, no study has ever been conducted in East Malaysia on childhood obesity. This study was aimed to determine the prevalence of child-hood obesity and to investigate the association of physical activity levels with obesity and its intervention among primary school children in Kota Kinabalu. Methods: A cross-sectional study involving 484 students (aged 7-12 years old) was conducted in five primary schools at Kota Kinabalu, Sabah. The schools were selected based on cluster sampling method and simple random sampling method. Primary school children with a known medical condition such as bronchial asthma, type-1 diabetes mellitus or those with a prolonged use of oral steroids was excluded from the study. Self developed questionnaires were used to record sociodemographic details and anthropometric mea-sures both parents and children, and physical activity was measured using a Children Physical Activity Questionnaire (C-PAQ). The intervention involved 3 components; I) motivational interviewing, ii) brief and focused advice, iii) ac-tivity session. Follow up was done 3 months after the intervention was conducted. Results: The prevalence of child-hood obesity among primary school children is 13.2%. There is a negative correlation between children’s BMI and amount of physical activity (-0.347) and positive correlation between children’s BMI and amount of non-physical activity (0.339). Little changes in the BMI of the children after intervention, t(127)= 2.866, p=0.005. Conclusion: This study provides evidence that childhood obesity is not a prevalent health problem in Kota Kinabalu and has proved that physical activity levels have significant associations with children’s body mass indices.