Bidirectional cavopulmonary shunt (BCPS) has played an important role in the staged Fontan approach; however, the timing remains controversial, especially in younger patients. Therefore, we examined the outcomes of BCPS in infants younger than 3 months of age. From 2004 to 2018, 120 patients underwent BCPS at <4 months of age (younger group). For reference, we also reviewed the data from 204 patients who had undergone the BCPS procedure during the same period at more than 4 months of age (older group). The median age and body weight at the time of the BCPS were 102 days and 4.2 kg for the younger group versus 196 days and 6.3 kg for the older group, respectively. Forty-eight patients (14.8%, 48 of 324; 16 in the younger group, 32 in the older group) had primary BCPS; the remaining 276 (104 in younger group, 172 in older group) had various forms of single-ventricle palliation before the BCPS procedure. Although preoperatively, 7 patients required extracorporeal membrane oxygenation (ECMO) support due to haemodynamic instability, they were successfully weaned from ECMO through haemodynamic benefits after BCPS. The 10-year actual survival rate (Kaplan-Meier) was 89% in the younger group and 86% in the older group (P = 0.55). Atrioventricular valve regurgitation (AVVR) was identified as a factor associated with hospital deaths in the younger group (P = 0.009), and much older age at BCPS was associated with late deaths in the older group (P = 0.027). In this study population, early performance of BCPS is applicable for patients who have undergone prior palliation and for those in whom primary BCPS is the first surgical intervention, even for patients with haemodynamic instabilities.