Childhood obesity has reached epidemic proportions in many parts of the world. This epidemic has also affected children and adults with congenital heart disease (CHD). Over one quarter of children with CHD are overweight or obese. Important comorbidities are associated with obesity including type 2 diabetes, systemic hypertension, hyperlipidemia, and obstructive sleep apnea. Obese children with CHD often have the traditional risk factors such as genetic predisposition, sedentary lifestyle, and poor dietary habits. However, they may also have unique risk factors such as higher caloric needs in early infancy and exercise restriction in childhood. Similar to children with normal hearts, those with CHD have higher left ventricular mass and abnormal vascular function and are more likely to have systemic hypertension. In the long term, these comorbidities may have a more profound effect on children who have underlying functional and/or anatomical abnormalities of the heart. As more children with CHD are now surviving into adulthood, investigating therapeutic interventions to treat and prevent obesity in this population is of utmost importance. Recommendations for safe physical activity, recreation sport, and exercise training for children with CHD have recently been published. These guidelines may help health care providers to change their practice of exercise restriction.