We report the case of a 11-year-old girl with Moyamoya syndrome, who had undergone staged-repair of tricuspid atresia to a Fontan circulation, scheduled to undergo bilateral pial synangiosis. Surgery for the first hemisphere was complicated by intracranial hemorrhage requiring an emergency craniotomy. The case highlights the importance of understanding Fontan physiology and its interrelationship with the cerebral circulation in the setting of cerebrovascular insufficiency and raised intracranial pressure.