Obesity in childhood and adolescence represents one of the most challenging public health problems of the 21st century owing to its epidemic proportions worldwide and the associated significant morbidity, mortality and public health costs. In Greece, the prevalence of overweight and obesity in childhood and adolescence exceeds 30–35%. To address the increasing prevalence of overweight and obesity in children and adolescents in our country, we developed the ‘National e-Health Program for the Prevention and Management of Overweight and Obesity in Childhood and Adolescence’, which provides specific and detailed guidance to all primary health care physicians about the personalized management of children and adolescents with overweight or obesity. In the present study we evaluated 2400 children and adolescents [mean age ± SEM: 10.10 ± 0.09 years.; Males: 1088, Females: 1312; Obesity (n = 1370, 57.1%), Overweight (n = 674, 28.1%), normal BMI (n = 356, 14.8%)], who followed the personalized multi-disciplinary management plan specified by the ‘National e-Health Program for the Prevention and Management of Overweight and Obesity in Childhood and Adolescence’, and were studied prospectively for 1 year. We demonstrated that at the end of the first year, the prevalence of obesity decreased by 32.1%, the prevalence of overweight decreased by 26.7%, and the cardiometabolic risk factors improved significantly. These findings indicate that our National e-Health Program is effective at reducing the prevalence of overweight and obesity in childhood and adolescence after one year of intervention in the largest sample size reported to date.