In the pediatric population, exercise capacity differs between females and males and the gap widens through adolescence. However, specific age- and sex-based changes in adolescents with congenital heart disease and Fontan palliation have not been reported. The purpose of the current study is to identify age- and sex-specific changes in exercise performance at peak and ventilatory anaerobic threshold (AT) for adolescents with Fontan physiology. Retrospective review of the Pediatric Heart Network Fontan cross sectional study (Fontan 1) public use dataset. Comparisons were made for peak and AT exercise parameters for females and males at 2-year age intervals. In addition, normative values were generated by sex and age at 2-year intervals. χ² test was used for comparison for categorical variables. Changes in exercise parameters between age groups by sex were compared by ANOVA with post-hoc analysis. Exercise testing was performed in 411 patients. AT was reached in 317 subjects (40% female), of whom, 166 (43% female) reached peak exercise. Peak oxygen consumption decreased 32% through adolescence in females and did not have the typical increase through adolescence for males. Oxygen consumption at AT also decreased with age in both sexes. In conclusion, age- and sex-based exercise performance for adolescents with Fontan physiology are predictably low, but there are additional significant decreases through adolescence for this population, especially in females. We have established normative exercise values for several parameters for this population which will better identify at risk patients and allow for earlier intervention.