Increasing habitual exercise has been associated with improved cardiopulmonary exercise testing (CPET) performance, specifically maximal oxygen consumption in children with operatively corrected congenital heart disease. This has not been studied in children following Fontan palliation, a population in whom CPET performance is dramatically diminished. A single-center cross-sectional study with prospective and retrospective data collection was performed that assessed habitual exercise preceding a clinically indicated CPET in children and adolescents with Fontan palliation, transposition of the great arteries following arterial switch operation (TGA), and normal cardiac anatomy without prior operation. Data from contemporaneous clinical reports and imaging studies were collected. The association between percent predicted VO_2max and habitual exercise duration adjusted for known covariates was tested. A total of 175 subjects (75 post-Fontan, 20 with TGA, and 80 with normal cardiac anatomy) were enrolled. VO_2max was lower in the Fontan group than patients with normal cardiac anatomy (p < 0.0001) or TGA (p < 0.0001). In Fontan subjects, both univariate and multivariate analysis failed to demonstrate a significant association between habitual exercise and VO_2max (p = 0.6), in sharp contrast to cardiac normal subjects. In multivariate analysis, increasing age was the only independent risk factor associated with decreasing VO_2max in the Fontan group (p = 0.003). Habitual exercise was not associated with VO_2max in subjects with a Fontan as compared to biventricular circulation. Further research is necessary to understand why their habitual exercise is ineffective and/or what aspects of the Fontan circulation disrupt this association.