Background: Some local governments have implemented strategies to increase physical activity as a way to control obesity 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 cardiovascular fitness in 12-14-year-old boy students. Methods: This study showed an intervention effect on some health-related fitness factors in students. A number of 127 boy students aged 12-14 years, in the city of Isfahan, based on preventive plan of inactivity in children at the provincial Health office selected randomly as subjects. Measurement variables include; weight, height, body mass index (BMI), waist-hip ratio (WHR), body-fat percent and aerobic power of subjects measured by valid tests. Results: This study revealed that body-fat percentage of this students changed near to 17.84% (42.25% pretest vs. 34.71% posttest), WHR 0.44%, (0.915 pretest vs. 0.911 posttest), VO 2 max changed 8.54% (27.84 pretest vs. 30.22 posttest) whereas BMI was changed 2.61% (26.81 pretest vs. 26.03 posttest). Results also revealed that there were significant differences between fat percent, (P = 0.001) and VO 2 max (P = 0.001), but there was no difference between BMI of subjects in pre and posttests (P = 0.452). Conclusions: Findings of this study signify that an implementation of short-term intervention components in the school system may have a beneficial effect on body-fat percentage and cardiovascular fitness of overweight/obese children.