At rest, a good Fontan circulation can provide a normal cardiac output (CO). However, as a consequence of its unique hemodynamic nature, the limitations of the Fontan circuit are exposed during exercise. We aimed to provide a comprehensive assessment of the pathophysiology of exercise in adult Fontan patients (FPs) and identify factors limiting their functional capacity (FC). In a single-center study conducted in 37 FPs aged ≥16 years and 19 healthy-controls (HCs) who underwent CPET on a cycle ergometer in February and March 2022, the mean peakVO2 was 21 ± 5.4 mL/kg/min, which was 55% of the predicted value. Morphologically, the left single ventricle showed a higher peakVO2% predicted value (57.4 ± 14.4% vs. 43.4 ± 8.1%, p = 0.045). The factors associated with low peakVO2 values were an early flattened or descending O2 pulse at maximal exertion (52 ± 14% vs. 62 ± 12.5, p = 0.04 and 47.6 ± 9% vs. 60 ± 14, p = 0.018, respectively) and chronotropic insufficiency (53 ± 12% vs. 69.8 ± 20%, p = 0.008). The OUES was found to be a useful parameter to assess the FC in FPs in maximal and submaximal exercise testing. A strong positive correlation was observed between the %OUES and peakVO2%predicted (r = 0.726, p > 0.001). The lung function was impaired in the FPs, mostly with a mild restrictive pattern (56.8%). The FPs showed lower inspiratory muscle strength compared to the HCs but it was not statistically associated with either the peakVO2 or VE/VCO2 slope. Regular intense physical activity improves one’s FC. Although FPs have inspiratory muscle weakness, its impact on their FC is unclear. The peakVO2% predicted grew progressively higher as the level of physical activity increased (low level 49.5 ± 14%, moderate level 55 ± 12%, intense level 69 ± 20%).