The purpose of this study was to prevent obesity and provide needed material for them with step box exercise training program in schools. Also, this study observed how step box exercise affects health care issues of obese children and their bone mineral density. To achieve this purpose, 22 obese girls who went to S elementary school located in the D city were randomly chosen for the subject of this study. They were classified into training group(n=11) and control group(n=11), then measured physical fitness and bone mineral density in the pre and the post of exercise treatment. To identify the gap of change amount according to the existence of exercise treatment, this study respectively conducted the paired sample t-test and independent sample t-test using SPSS WIN Ver. 18.0 statistics program. The results are as follows; First, 12-week step box exercise helped obese elementary school girl students of improving the cardiovascular endurance, muscular endurance and % body fat. During 12 weeks, exercise group was shown significant differences, but was no changes in the control group of three elements. Secondly, step box exercise was not contributed to bone mineral density increase of obese girl students during 12 weeks. Considering the characteristics of bone mineral density which has no large changes in a short period. In conclusion, step box exercise training was effective for the enhancement of physical fitness(cardiovascular endurance, muscular endurance, % body fat), but not effective for the improvement of bone mineral density. This program will be expected to contribute to improvement of physical fitness and obesity for obese children through the providing it develop and apply in various and complementary ways.