BackgroundDespite the improved management of patients with a single ventricle, the long-term outcomes are not optimal. We reported the outcomes of the bidirectional Glenn procedure (BDG) and factors affecting the length of hospital stay, operative mortality, and Nakata index before Fontan completion.ResultsThis retrospective study included 259 patients who underwent BDG shunt from 2002 to 2020. The primary study outcomes were operative mortality, duration of hospital stay, and Nakata index before Fontan. Mortality occurred in 10 patients after BDG shunt (3.86%). By univariable logistic regression analysis, postoperative mortality after BDG shunt was associated with high preoperative mean pulmonary artery pressure (OR: 1.06 (95% CI 1.01–1.23);P= 0.02). The median duration of hospital stay after BDG shunt was 12 (9–19) days. Multivariable analysis indicated that Norwood palliation before BDG shunt was significantly associated with prolonged hospital stay (β: 0.53 (95% CI 0.12–0.95),P= 0.01). Fontan completion was performed in 144 patients (50.03%), and the pre-Fontan Nataka index was 173 (130.92–225.34) mm2/m2. Norwood palliation (β: − 0.61 (95% CI 62.63–20.18),P= 0.003) and preoperative saturation (β: − 2.38 (95% CI − 4.49–0.26),P= 0.03) were inversely associated with pre-Fontan Nakata index in patients who had Fontan completion.ConclusionsBDG had a low mortality rate. Pulmonary artery pressure, Norwood palliation, cardiopulmonary bypass time, and pre-BDG shunt saturation were key factors associated with post-BDG outcomes in our series.