Children born with univentricular hearts undergo staged surgical procedures to a Fontan circulation. Long‐term experience with Fontan palliation has shown dramatically improved survival but also of a life‐long burden of an abnormal circulation with significant morbidity. Many Fontan patients have reduced exercise capacity, oxygen uptake, lung function and quality of life. Endurance training may improve submaximal, but not maximal, exercise capacity, lung function and quality of life. Physical activity and endurance training is also positively correlated with sleep quality. Reviewing the literature and from our single‐centre experience, we believe there is enough evidence to support structured individualised endurance training in most young Fontan patients.