In order to test the effect of systematic supervised physical training, we divided a total of 129 children and adolescents with congenital heart disease into a group undergoing intervention and a control group. All patients underwent exercise tests, measurements of physical activity, and a survey of psychosocial factors. An improvement in uptake of peak level of oxygen was observed after intervention. There was also an improvement in physical activity in both groups measured by a monitor, although this was significant only in those with intervention. The psychosocial scales measured by the Child Behavior Checklist showed a decrease in internalizing scores for those subjected to intervention. This was decreased due to decreased withdrawal and somatic complaints. In conclusion, we recommend systematic supervised training, including testing of routine follow-ups, in patients with congenital heart disease.