Functionally single ventricle with major aortopulmonary collateral arteries and pulmonary atresia is very rare. Surgical indication for this combination of abnormalities is still unclear and Fontan procedure is still a crucial challenge for the patient who has this anomaly. We report a case with asplenia, functionally single ventricle, pulmonary artesian and pulmonary abnormal arborization who successfully underwent staged Fontan operation. In this case, the left upper lobe area, where the flow from a Glenn shunt was overwhelmed by the collateral arterial blood flow, was excluded from the Fontan circulation by the ligation of the left upper pulmonary arterial branch at its most proximal side at the time of fenestrated extracardiac total cavopulmonary connection.