This study aimed to identify its influence on pulmonary development and hemodynamics before bidirectional Glenn (BDG) anastomosis. This retrospective study involved 30 consecutive patients with univentricular hearts who underwent bilateral pulmonary artery banding (bil-PAB) and BDG anastomosis between September 2011 and September 2018 at our institution. These patients were classified into the nitrogen (N = 12) and no nitrogen (N = 18) groups according to their use of hypoxic gas therapy. Clinical echocardiographic, operative, and catheter examination data were reviewed. Nakata index was 131 (110–167) in the nitrogen group and 138 (88.4–161.7) in the no nitrogen group (P = 0.8). Pulmonary vascular resistance (PVR) was 1.50 (1.30–2.4) in the nitrogen group and 138 (88.4–161.7) in the no nitrogen group (P = 0.3). There was no statistical difference between the pulmonary development in both groups. In the subgroup of hypoplastic left heart syndrome patients, there was a statistical difference. RVEDV% of normal was 232.5 (215–239) in the nitrogen group and 201 (161–209) in the no nitrogen group (P = 0.03). Pulmonary development was not significantly different when hypoxic gas therapy was performed using nitrogen vs. not using nitrogen. However, RVEDV% of normal might be larger with hypoxic gas therapy using nitrogen. Although there is no obvious systemic atrioventricular valve regurgitation exacerbation with hypoxic gas therapy, it might be useful to prevent a decrease in PVR and may also affect bil-PAB and subclinical increase in systemic atrioventricular valve regurgitation.