Aim A growing number of patients with Fontan circulation are reaching adulthood, and there is increasing concern about their physical performance and quality of life. This study compared self‐reported exercise and measured activity with quality of life in patients after Fontan palliation and healthy controls. Methods Physical exercise during an average school week was reported by 30 Fontan circulation patients aged eight to 20 years, and 25 healthy controls, followed by accelerometer recordings over seven days. All subjects and their parents answered a questionnaire on quality of life. Results Patients reported spending less time exercising each week than the controls (114 ± 66 minutes vs. 228 ± 147 minutes, p < 0.001). However, the overall measured activity and moderate‐to‐vigorous activity was similar for patients and controls. Patients reported a lower quality of life score than the controls (70.9 ± 9.9 vs. 85.7 ± 8.0, p < 0.001). Conclusion In spite of similar measured total activity, Fontan patients reported less time engaged in regular physical exercise than healthy controls and their quality of life was lower than the controls. We speculate that promoting structured regular physical exercise could improve the quality of life of Fontan patients.