This case report describes a young female patient with a history of surgery to treat choledochal cyst since childhood who was admitted to our hospital with cholangitis. An imaging examination revealed giant stones that almost completely filled the intrahepatic biliary tract. The patient underwent percutaneous transhepatic lithotripsy using a holmium laser. After the lithotripsy, cholangiography showed no residual stones. The patient displayed clinical improvement and was discharged after 14 days in the hospital. This case serves as a reminder of gallstone complications that can occur subsequent to choledochal cyst surgery with biliary-enteric anastomosis and emphasizes many outstanding advantages of percutaneous transhepatic lithotripsy compared with classical surgery.