Choledochal cysts are not rare in East Asia. The classic symptoms of these cysts are intermittent abdominal pain, jaundice, and a right upper quadrant abdominal mass. The authors report the case of an infant with a choledochal cyst presenting with intracranial hemorrhage. This 2-month-old girl with a partial coma presented at the authors' hospital. A brain CT scan revealed right-sided subdural hemorrhage. The routine preoperative survey found coagulopathy. After correcting the bleeding disorder, an emergency craniectomy was performed. Further examination found a choledochal cyst during abdominal ultrasonography and CT. Choledochal cysts are a cause of neonatal cholestasis but rarely produce vitamin K deficiency bleeding.