Exercise performance declines as patients who have undergone Fontan operation enter adolescence. However, the effect of altitude on functional capacity after Fontan remains inadequately studied. Our aim was to describe exercise performance in a cohort of patients with Fontan physiology living at increased altitude and compare to a normal control group and relate these data to invasively derived hemodynamics. We hypothesized that peak oxygen consumption (\(V_{{{\text{O}}_{2} {\text{peak}}}}\)) would be decreased, in association with elevated mean pulmonary artery pressure (mPAP) and pulmonary vascular resistance (PVRi). Patients were evaluated in a multidisciplinary clinic for patients with Fontan physiology. Evaluation included cardiopulmonary exercise test and cardiac catheterization at predetermined intervals. Descriptive statistics were calculated. Associations of catheterization and exercise testing measures with \(V_{{{\text{O}}_{2} {\text{peak}}}}\) were estimated with Spearman correlation coefficients. One hundred patients with age- and gender-matched controls were included in the analysis. The mean age was 13.3 ± 3.9 years, with mean weight of 47.1 ± 18.4 kg. The mean \(V_{{{\text{O}}_{2} {\text{peak}}}}\) was 29.0 ± 7.8 ml/kg/min, significantly lower than the control group, 40.2 ± 8.4 ml/kg/min (p < 0.0001). There was no statistically significant linear correlation between \(V_{{{\text{O}}_{2} {\text{peak}}}}\) and mPAP or PVRi. We characterized exercise performance in a large cohort with Fontan physiology living at increased altitude and showed a decrease in \(V_{{{\text{O}}_{2} {\text{peak}}}}\) compared to controls. Our data do not support the hypothesis that moderately increased altitude has a detrimental effect on exercise performance, nor is there a substantial link between poor cavopulmonary hemodynamics and exercise in this setting.