Misalignment of pulmonary veins with alveolar capillary dysplasia (MPV) has been reported to be a rare cause of persistent pulmonary hypertension of the newborn (PPHN) and to be fatal despite extracorporeal membrane oxygenation (ECMO). A full-term female neonate with PPHN was brought to the hospital for ECMO therapy at 2 days of age. On the 14th day of life, she was extubated early after the second run of ECMO, and underwent nitric oxide (NO) inhalation therapy in the incubator. She died of catheter-related sepsis on the 61st day of life. After autopsy findings revealed MPV, the longest survival with this disease was documented. NO inhalation therapy in the incubator may provide time for lung transplantation.