Objective: This study aimed to elucidate the postoperative particular issues of congenital dilatation of the intra- and extrahepatic bile duct (Todani type IV-A congenital choledochal cyst (CCC)) with pancreaticobiliary maljunction. Methods: 17 patients with intrahepatic stones (IHS) developed after flow-diversion surgery (excision of the extrahepatic bile duct and reconstruction) for type IV-A CCC were treated in our department between 1974 and 2015. Flow-diversion surgery was performed at our department in 6 patients and at other hospitals in 11 patients. We examined postsurgical treatment scores regarding hepatolithiasis. Results: The median time of IHS confirmation from flow-diversion surgery was 9.9 years (range: 1–20 years). Most cases presented with cholangitis. Morphologically, persistence of intrahepatic bile duct dilatation and stricture and anastomotic stricture at the hepaticoenterostomy were seen in all cases and 7 patients, respectively. Stone removal, reconstruction with choledocho-enterostomy or hepatectomy were performed for IHS. Although prognosis was good in patients with well-controlled jaundice and cholangitis, 3 patients died with liver failure due to cholestatic liver cirrhosis. Conclusion: IHS formation was considered to be largely ascribable to cholestasis caused by persistence of intrahepatic bile duct dilatation and stricture. To avoid postoperative cholestasis, adding hepatic duct plasty and creating a wide anastomosis are required when performing flow diversion surgery. Early stone removal and resolution of cholestasis to control cholangitis and jaundice is important in case IHS occurs after flow diversion surgery.