Childhood obesity causes a higher risk of obesity, premature death and disability in adulthood. In addition, obese children experience an increased risk of respiratory problems, hypertension, cardiovascular disease, insulin resistance and psychological effects. This study aimed to investigate how an exercise intervention affects health-related physical fitness and inflammatory-related blood factors in obese children after. We hypothesized that there would be positive effects on serum levels of insulin-like growth factor-1 (IGF-1), connecting peptide(C-peptide) and resistin, as well as in muscle and cardiovascular-related physical capacities, after an exercise intervention in obese children. Thirty-seven obese children haveperformed health-related fitness tests and provided blood samples for the analysis of changes in circulating biomarkers, both before and after an 8-week exercise intervention, which includes stretching, aerobic exercise, resistance exercise and sports games. The results indicate that exercise training beneficially affects body compositions, especially percentage body fat and muscle mass, without influencing to body weight and height. The results of the physical fitness tests show that muscle and cardiovascular capacity were increased in obese children in response to exercise training. Simultaneously, the exercise training decreased circulating levels of C-peptide, which equated to a “large” effect size. Although there were no significant effects on the levels of IGF-1 and resistin, they show a “small” effect size. Therefore, our findings suggest that the exercise intervention have beneficial effects on body composition and physical fitness levels in obese children, whichmight be associated with the decline in circulating C-peptide.