Background The incidence of choledochal cyst with intrahepatic involvement (Todani's type IV-A cyst) is considerably high. Dilatation of the intrahepatic bile duct is frequently observed around the hepatic hilum, occasionally in the umbilical portion, and rarely in the more upstream intrahepatic bile duct, associated with or without downstream stricture. We recently encountered 2 children with type IV-A cyst associated with upstream intrahepatic ductal dilatation; one with a cystic dilatation of the medial branch arising from the left hepatic duct and another with a cyst of the medial branch arising from the anterior hepatic duct. Methods After excision of the extrahepatic bile duct cyst at the hilum and making a large fenestration of the intrahepatic duct cyst, hepaticojejunostomy and intrahepatic cystojejunostomy were performed using a Roux-en-Y jejunal loop in both children. Results Postoperatively, both intrahepatic cysts were remarkably reduced in size, and recurrent bouts of abdominal pain did not occur for up to 4 or 5 years. Conclusion Hepaticojejunostomy at the hepatic hilum, combined with intrahepatic cystojejunostomy, appears to be a recommendable procedure for an upstream intrahepatic ductal cyst of type IV-A, preventing postoperative cholangitis owing to bile stone formation.