To study physical activity and sleep in Fontan patients and healthy controls before and after an endurance training program, and after 1 year. Fontan patients (n = 30) and healthy controls (n = 25) wore accelerometers for seven consecutive days and nights during a school week before and after a 12-week endurance training program and after 1 year. Patients had similar sleep duration and sleep efficiency as healthy controls. Latency to sleep onset in minutes was longer for patients than controls (22.4 (4.3-55.3) minutes versus 14.8 (8.6-29.4) minutes, p < 0.01). More time in moderate-to-vigorous activity daytime was correlated with increased sleep time (p < 0.05; r2 = 0.20), improved sleep efficiency (p < 0.01; r2 = 0.24) and less time as wake after sleep onset (p < 0.05; r2 = 0.21) for patients but not controls. Sleep variables did not change after the exercise intervention for patients or controls. After 1 year, patients had decreased total sleep time, decreased sleep efficiency, increased accelerometer counts during sleep and more time as wake after sleep onset during sleep time, but not controls. Fontan patients have prolonged latency to sleep onset compared with controls. More time in physical activities was correlated with better sleep quality for the patients. Also, subjects with low sleep efficiency and long latency to sleep onset may benefit most from physical exercise. These patients should be encouraged to engage in individually designed physical exercise as this could improve sleep quality.