Objective: To evaluate the cost effectiveness of a school based comprehensive intervention for childhood obesity and to provide scientific basis for formulating and promoting efficient and economic intervention measures for childhood obesity. Methods: In a cluster randomized controlled trial, 12 primary schools (1 889 students from grade 3 to 5) in Dongcheng District in Beijing were selected and randomly assigned to the intervention (6 schools, 930 students) and control group (6 schools, 959 students). Students in the intervention group received a one year school based comprehensive intervention for childhood obesity, including development of school level policies, health education activities, improvement of physical activity, and improvement of healthy diet. A cost analysis method from a social perspective was used to evaluate the implementation costs of the intervention. Cost effectiveness analysis was used by calculating incremental cost effectiveness ratio (ICER) on obesity related knowledge, number of days completing no less than 60 minutes of moderate to vigorous physical activity (MVPA) per week, students consuming sugar sweetened beverage. Results: The material cost and human cost were 46 376.24 yuan and 46 197.32 yuan, respectively. The total cost of the intervention was 92 573.56 yuan and the average cost was 99.54 yuan per student in the intervention group. ICER on obesity related knowledge, number of days completing no less than 60 minutes of MVPA per week, percentage of students consuming sugar sweetened beverage were 52.39%, 71.61% and 2.26%, respectively. Conclusion The school based comprehensive intervention for childhood obesity shows a good cost effectiveness promoting students obesity related knowledge, as well as dietary and physical activity behaviors.