In 2014, our hospital introduced inhaled nitric oxide (iNO) therapy combined with high-flow nasal cannula (HFNC) oxygen therapy after extubation following the Fontan procedure in patients with unstable hemodynamics. We report the benefits of HFNC-iNO therapy in these patients. This was a single-center, retrospective review of 38 patients who underwent the Fontan procedure between January 2010 and June 2016, and required iNO therapy before extubation. The patients were divided into two groups: patients in Epoch 1 (n = 24) were treated between January 2010 and December 2013, receiving only iNO therapy; patients in Epoch 2 (n = 14) were treated between January 2014 and June 2016, receiving iNO therapy and additional HFNC-iNO therapy after extubation. There were no significant differences between Epoch 1 and 2 regarding preoperative cardiac function, age at surgery, body weight, initial diagnosis (hypoplastic left heart syndrome, 4 vs. 2; total anomalous pulmonary venous return, 5 vs. 4; heterotaxy, 7 vs. 8), intraoperative fluid balance, or central venous pressure upon admission to the intensive care unit. Epoch 2 had a significantly shorter duration of postoperative intubation [7.2 (3.7–49) vs. 3.5 (3.0–4.6) hours, p = 0.033], pleural drainage [23 (13–34) vs. 9.5 (8.3–18) days, p = 0.007], and postoperative hospitalization [36 (29–49) vs. 27 (22–36) days, p = 0.017]. Two patients in Epoch 1 (8.3%), but none in Epoch 2, required re-intubation. Our results suggest that HFNC-iNO therapy reduces the duration of postoperative intubation, pleural drainage, and hospitalization.