Background The surgical outcomes of hypoplastic left heart syndrome with intact atrial septum remains very poor in spite of the introduction of prenatal diagnosis before the Norwood operation. The hybrid operation consisting of bilateral pulmonary artery banding and balloon atrioseptectomy is one of the treatment strategies to potentially improve this patient population, however, the long-term outcomes are unknown. Methods Six consecutive patients with hypoplastic left heart syndrome with intact atrial septum, who underwent the hybrid operation between October 2006 and July 2014, were retrospectively reviewed. Hypoplastic left heart syndrome with highly restrictive atrial communication was excluded. Results Three patients died after the hybrid operation, due to sepsis, cerebral bleeding, and heart failure. Three patients underwent the modified Norwood operation. One of these died due to severe hypoxia while awaiting the bidirectional Glenn operation. The others underwent a bidirectional Glenn operation and subsequent Fontan completion but died due to lung dysfunction and sudden hemoptysis. Conclusions The hybrid operation for hypoplastic left heart syndrome with intact atrial septum may have improved the neonatal outcome and Fontan completion rate in this extremely high-risk group of patients, but the long-term outcome remains dismal. Considering the late mortality related to pulmonary complications, aggressive fetal intervention to create a nonrestrictive atrial septal communication to promote normal development of the pulmonary vessels may be the last resort to improve the long-term outcome.