Fontan palliation allows patients with “single ventricle” circulation to reach adulthood with an acceptable quality of life, although exercise tolerance is significantly reduced. To assess whether controlled respiratory training (CRT) increases cardiorespiratory performance. 16 Adolescent Fontan patients (age 17. 5 ± 3.8 years) were enrolled. Patients were divided into CRT group (n = 10) and control group (C group, n = 6). Maximal cardiopulmonary test (CPT) was repeated at the end of CRT in the CRT group and after an average time of 3 months in the C group. In the CRT group a CPT endurance was also performed before and after CRT. In the CRT group there was a significant improvement in cardiovascular and respiratory response to exercise after CRT. Actually, after accounting for baseline values, the CRT group had decreased breathing respiratory reserve (− 15, 95% CI −22.3 to − 8.0, p = 0.001) and increased RR peak (+ 4.8, 95% CI 0.7–8.9, p = 0.03), VE peak (+ 13.7, 95% CI 5.6–21.7, p = 0.004), VO₂ of predicted (+ 8.5, 95% CI 0.1–17.0, p = 0.05), VO₂ peak (+ 4.3, 95% CI 0.3 to 8.2, p = 0.04), and VO₂ workslope (+ 1.7, 95% CI 0.3–3.1, p = 0.02) as compared to the control group. Moreover, exercise endurance time increased from 8.45 to 17.7 min (p = 0.01). CRT improves cardiorespiratory performance in post-Fontan patients leading to a better aerobic capacity.