The pulmonary artery anatomy is one of the important determinants of Fontan completion and its outcomes in patients with functionally univentricular hearts. Despite several modifications to Fontan operation, unbalanced pulmonary arteries pose a significant challenge in this subset of patients. Intrapulmonary artery septation is a technique, developed to rehabilitate the unilateral hypoplastic pulmonary artery following various initial palliative procedures in functionally univentricular hearts. Literature is sparse on this technique. This article reviews the basic concepts and literature on intrapulmonary artery septation. We also describe our experience with modified intrapulmonary artery septation.