Central factors negatively affect the functional capacity of Fontan patients (FP), but “non-cardiac” factors, such as pulmonary function, may contribute to their exercise intolerance. We studied the pulmonary function in asymptomatic FP and its correlations with their functional capacity. Pulmonary function and cardiopulmonary exercise tests were performed in a prospective study of 27 FP and 27 healthy controls (HC). Cardiovascular magnetic resonance was used to evaluate the Fontan circulation. The mean age at tests, the mean age at surgery, and the median follow-up time of FP were 20(±6), 8(±3), and 11(8–17) years, respectively. Dominant ventricle ejection fraction was within normal range. The mean of peak VO₂ expressed in absolute values (L/min), the relative values to body weight (mL/kg/min), and their predicted values were lower in FP compared with HC: 1.69 (±0.56) vs 2.81 (±0.77) L/min; 29.9 (±6.1) vs 41.5 (±9.3) mL/kg/min p < 0.001 and predicted VO₂ Peak [71% (±14) vs 100% (±20) p < 0.001]. The absolute and predicted values of the forced vital capacity (FVC), forced expiratory volume in one second (FEV₁), inspiratory capacity (IC), total lung capacity (TLC), diffusion capacity of carbon monoxide of the lung (DLCO), maximum inspiratory pressure (MIP), and sniff nasal inspiratory pressure (SNIP) were also significantly lower in the Fontan population compared to HC. An increased risk of restrictive ventilatory pattern was found in patients with postural deviations (OD:10.0, IC:1.02–97.5, p = 0.042). There was a strong correlation between pulmonary function and absolute peak VO₂ [FVC (r = 0.86, p < 0.001); FEV₁ (r = 0.83, p < 0.001); IC (r = 0.84, p < 0.001); TLC (r = 0.79, p < 0.001); and DLCO (r = 0.72, p < 0.001). The strength of the inspiratory muscles in absolute and predicted values was also reduced in FP [−79(±28) vs −109(±44) cmH₂O (p = 0.004) and 67(±26) vs 89(±36) % (p = 0.016)]. Thus, we concluded that the pulmonary function was impaired in clinically stable Fontan patients and the static and dynamic lung volumes were significantly reduced compared with HC. We also demonstrated a strong correlation between absolute Peak VO₂ with the FVC, FEV₁, TLC, and DLCO measured by complete pulmonary test.