Mortality from pulmonary agenesis is still high because of associated anomalies and respiratory complications during the neonatal period. In this report, a rare case of pulmonary agenesis in a neonate who was treated with ECMO is described. A full term baby boy was admitted to the hospital with the diagnosis of anorectal anomaly on the day of birth. The patient suddenly developed progressive respiratory distress on admission. A chest radiograph showed opacity of the right hemithorax with a shift of the mediastinum to the right. The patient fell into serious cardiopulmonary failure due to left pneumothorax following tracheal intubation. ECMO was started 20 hours after birth. The patient improved and was weaned from ECMO after 10 days. Further examination revealed total anomalous pulmonary venous drainage (TAPVD) and duodenal atresia. Although the patient died of heart failure after cardiac operation on the 29th day of age, ECMO was found to be a life-saving measure in pulmonary agenesis with respiratory complications in the early days of life.