BACKGROUND: In the past two decades, physical activity has decreased during both childhood and adolescence, and particularly adolescence. It seems that schools are attractive settings in which to implement interventions designed in order to promote physical activity in children; but in Iranian students, few studies have evaluated the effects of such interventions on overweight and obese children. The aim of this study was to evaluate the effects of a short-term school-based physical activity on obesity and aerobic fitness in 12-14 years aged girls. METHODS: This is a study with single group pretest and posttest design, in which 129 middle school girls in city of Isfahan were assessed based on preventive plan of inactivity in children at the Provincial Health Office. Variables, including weight, height, body mass index (BMI), waist-hip ratio (WHR), body fat percentage and aerobic power of subjects were measured using valid tests. RESULTS: This study showed that subjects' body fat percentage changed about 3.6% (37.74% pretest vs. 36.39% posttest), VO2 max changed 7.43% (29.72 pretest vs. 31.93 posttest), WHR changed 1.12% (0.89 pretest vs. 0.88 posttest), whereas BMI was changed 1.65% (27.80 pretest vs. 27.34 posttest). Findings also revealed that there were significant differences between fat percent, (P = 0.001) and VO2 max (P = 0.001) of subjects, but there was no difference between BMI of them in pre- and post-tests (P = 0.361). CONCLUSIONS: These results suggest that even a short-term exercise intervention may lead to positive changes in body fat percentage, WHR and aerobic fitness of overweight children. Therefore, school-based physical activity interventions can be an effective preventive strategy to control obesity and overweight in students.