Objective Exercise leads to the release of certain neurotransmitters in the brain that alleviate pain, both physical and mental status. Physical activity is associated with a range of positive health outcomes, including fewer depressive symptoms. Physical activity increases expression of BDNF, which may enhance brain health. But the effects of physical activity on brain nerve growth factors for children are not clear. Therefore, the purpose of this study was to determine the effects of physical activity and obesity factor on brain nerve growth factor in children. Methods Seventy-eight subjects were selected from one elementary school. We were measured variables of body composition, physical fitness, serum lipid, physical activity and brain nerve growth factor(insulin, BDNF, serotonin). The physical activity of day life changes were tested using the SenseWear Armband. The collected data were analyzed Total energy expenditure, Average METs, Time of 3.0 METs less than activity, Time of activity between 3.0 and 5.9 METs, Time of 6 METs over activity. The factors of brain nerve growth factor were BDNF (brain-derived neurotrophic factor), serotonin, insulin. Data analysis was done using PASW Statistics 18.0 program and included independent t-test, Pearson correlation coefficients and stepwise multiple regression. Results The results of this study were as follows, BDNF in obese children was lower than the normal children. Muscle mass and insulin, BDNF, percent muscle mass and BDNF, serotonin, time of 6 METs over activity and BDNF were positively correlated. Percent body fat and BDNF were negatively correlated. The variables predicting Insulin were muscle mass and cardiorespiratory endurance. And predictors of BDNF were the muscle mass and time of 6 METs over activity. And predictors of serotonin were the percent muscle mass and muscular strength. Conclusion The results indicate that it is necessary to improve brain nerve growth factor to increase muscle mass, time of 6 METs over activity in children.