Obesity is a chronic condition whose incidence is growing due to lack of exercise and frequent nutrition disorders. Childhood obesity has reached epidemic proportions worldwide. One of the best treatment methods is physical training. However, conflicting results have been reported regarding its clinical effectiveness. These contrasting findings may be due to the type and intensity of the adopted physical training program. Therefore, the purpose of the current study was to investigate the effect of an 8-week individualized physical training program on endothelial function, blood biomarkers and adipokine levels in obese children with and without metabolic syndrome (MS). One-hundred-and-twenty-two obese adolescents (71 obese without MS and 51 obese with MS) aged 14 ± 2 years were included in this study. The 8-week individualized training program decreased glucose, triglycerides, total cholesterol, low-density lipoprotein cholesterol and leptin in obese subjects with and without MS. However, adiponectin and endothelial-dependent vasodilatation increased in the follow-up study in both groups. Taken together, the findings suggest that individualized training program is an effective means for the treatment of obesity and MS in pediatric populations.