We report a case of recurrent gastritis with pyloric stenosis and cholangitis due to a rare variation in bile duct anatomy. A 72-year-old female patient showed recurrent gastral ulcers and biliary colic with cholangitis caused by gallstones in the main bile duct with an ectopic orifice in the prepyloric region and concurrent inflammatory pyloric stenosis. After temporarily successful endoscopic treatment with stenting and pyloric dilatation, the patient suffered from recurrent cholangitis. Finally, the abnormal biliary anatomy required surgical treatment with biliodigestive anastomosis.