Objective The bidirectional cavopulmonary shunt (BCPS) is an effective palliative procedure which has been widely used to boost outcome of the Fontan procedure. However, there is no standard duration time between these two procedures. Therefore, we investigated whether different time intervals between BCPS and Fontan procedure affects morbidity and mortality of Fontan patients. Methods Between 2004 and 2016, 210 post-BCPS patients underwent Fontan operation at Fuwai Hospital. The median interval between BCPS and Fontan procedure was 3.7 years (range 0.55-11.86 years) and this was used to divide study cohort into Group 1 (<3.7 years; n = 124) and Group 2 (>3.7 years; n = 86). We analyzed these patients retrospectively in terms of their preoperative characteristics and post-operative and follow-up results. Results Weight z-scores for age at BCPS (-0.731.39 vs -1.17 +/- 1.60, p < 0.05) was significantly higher in Group 2. However, saturation at room air before Fontan (76.42 +/- 20.01 vs 82.85 +/- 9.69, p < 0.001) was significantly higher in Group 1. The morbidity and mortality were similar between two groups. There were twelve hospital deaths (5.7%): eight (8/124, 6.5%) presented in Group 1 and four (4/86, 4.7%) in Group 2. On multi-variable analysis, risk factors for death were prolonged mechanical ventilation [hazard ratio (HR) 1.02, p = 0.004] and single right ventricle (HR 7.17, p = 0.03). After a mean follow-up of 4.95 years (range 0.74-13.62 years), one patient in Group 1 died of heart failure 13 months after Fontan procedure. The overall Fontan failure in Group 1 was similar to that in Group 2 (2.7% vs 2.6%, p = 0.985). The incidence of arrhythmias and re-intervention were not different between the two groups. Conclusions Fontan procedure could be performed safely in patient who stayed in long duration between Fontan procedure and BCPS without affecting the operative and long-term follow-up results. However, for post-BCPS patients with severe hypoxemia, earlier age at Fontan might be a good choice.