The Fontan procedure is the palliative surgical treatment for different congenital heart diseases (CHD) with a univentricular heart, but it has been associated with decreased exercise capacity, cardiovascular morbidity, and premature mortality. The one-and-half ventricle repair (1.5VR) was introduced as an alternative to the Fontan procedure, specifically for selected patients with borderline hypoplastic right ventricle (HRV), aiming for a more physiological circulation. Despite these efforts, the benefit of 1.5VR over Fontan circulation comparison on clinical and functional outcomes remains unclear. The aim of this study was to investigate and compare young patients with HRV after 1.5VR with those with functional single right or left ventricles (FSRV or FSLV) after Fontan palliation over a 10-year follow-up period. In this retrospective observational study, serial cardiopulmonary exercise tests (CPETs) performed in patients with 1.5VR and Fontan circulation between September 2002 and March 2024 have been analyzed. Only patients with at least 10 years of follow-up were considered. A total of 41 patients were included (age at baseline 8.6±2.6 years): 21 with FSLV, 12 with FSRV, and 10 with 1.5VR. No differences in cardiorespiratory fitness and efficiency were shown at the first CPET assessment among the three groups. At 10-year follow-up, 1.5VR had higher cardiorespiratory fitness and efficiency compared to FSLV and FSRV patients. These findings suggest that the 1.5VR may provide superior long-term functional outcomes than the Fontan procedure in patients with borderline HRV. Further studies are needed to evaluate the impact on hard clinical endpoints.