Management of complications in patients with Roux-en-Y reconstruction is still today an important surgical and endoscopic challenge. Various techniques have been employed to manage biliary strictures and intrahepatic calculi in patients with Roux-en-Y hepaticojejunostomy (RYHJ). We report the case of a 24-year-old female who had undergone RYHJ reconstruction 3 years back for choledochal cyst, admitted with the diagnosis of obstructive jaundice due to anastomotic stricture and multiple hepatic duct calculi. She was successfully treated with laparoscopic-assisted transjejunal endoscopic management of intrahepatic calculi and anastomotic stricture, which appears to be safe and useful procedure for anastomotic stricture and hepatic duct calculi in patients with surgically altered anatomy.