Purpose Physical activity and a healthy lifestyle play an essential role in optimizing long-term health in patients with Fontan physiology. Wrist-worn activity trackers may be useful in medically directed exercise programs for patients with Fontan physiology. The objective of this study was to measure the validity of Garmin and Fitbit activity tracker heart rate detection in patients with Fontan circulation when compared with electrocardiogram during cardiopulmonary exercise testing (CPET). Methods Forty-seven Fontan patients undergoing CPET for clinical indications were included and wore activity trackers during CPET. Heart rate via the activity tracker was collected at baseline, maximal exercise, and recovery. Patient heart rates, peak VO2, and peak respiratory exchange ratio were collected using standard CPET protocols and equipment. Heart rate at each time point was compared between the activity trackers and CPET electrocardiogram. Results Median age of participants was 17.1 yr, 15.1 yr since Fontan completion. Mean percentage of predicted peak VO2 was 56.8%, with a z-score of -3.2, and 61.7% of participants completing a maximal CPET. Baseline mean oxygen saturation was 92.9% and 90.0% at maximal exercise. Activity trackers demonstrated mean absolute percentage error <10% at most time points, comparable with other studies. Demographics, Fontan-associated comorbidities, and echocardiogram findings did not impact the accuracy. Conclusions Consumer-oriented wrist-worn activity trackers show promising accuracy for heart rate monitoring in medically directed exercise programs for adolescents and young adults with Fontan physiology. Further validation across different exercise modalities is needed.