Background: Most Fontan patients have impaired exercise capacity, and a further decline in exercise capacity over time seems inevitable. However, few longitudinal studies exist, and there is a lack of data from newer eras. We aimed to describe the natural evolution of exercise capacity over a 10-year period in a contemporary, population-based cohort of Danish Fontan patients. Methods: The study was a nationwide, prospective study. A cardiopulmonary exercise test (CPET) was used to assess the exercise capacity. All Danish Fontan patients who participated in a national study in 2011 (CPET1), were invited to a follow-up visit in 2021 (CPET2). All patients who completed CPET1 and CPET2 with a respiratory exchange ratio over 1.0 were included. The main outcome was percent predicted VO2_peak (%pred VO2_peak). At the time of CPET2, patients filled out a questionnaire including questions regarding physical activity. Results: Seventy-seven patients completed both CPET1 and CPET2, and seventy patients completed the questionnaire. The time interval between the two CPETs was 10.4 ± 0.9 years. The median age was 15 years at CPET1 and 26 years at CPET2. The exercise capacity remained stable with a mean %pred VO2_peak of 53.8 ± 11.3 at CPET1 and 55.6 ± 10.9 in CPET2 (p = 0.314). Higher levels of vigorous physical activity were associated with higher %pred VO2_peak in CPET2 in a multivariate regression model. Conclusion: The %pred VO2peak remained stable over a ten-year period in this population-based Fontan cohort. Higher levels of self-reported vigorous physical activity were associated with higher %pred VO2_peak in the most recent CPET.