A 50-year-old female who was otherwise healthy was admitted to the hospital due to a complaint of right upper quadrant abdominal pain for more than 10 days. The patient did not have nausea, vomiting, or fever. The patient’s pain did not improve after rest. Then, she went to the local hospital, where she was initially diagnosed with pancreatitis. She felt slightly better after symptomatic treatment. At the same time, CT revealed choledochal cysts. Therefore, she was admitted to our hospital for further evaluation and treatment. Physical examination showed mild tenderness in the right upper abdomen. There was neither rebounding pain nor jaundice. No hepatosplenomegaly was detected. Her haematology and biochemistry investigations were otherwise unremarkable except for an increased amylase level of 213 U/L. She had no known family history of biliary diseases, and she did not have any chronic diseases. Magnetic resonance cholangiopancreatography showed that the common bile duct was thickened and dilated with a diameter of approximately 20 mm. There was no content inside or obvious expansion of the intrahepatic bile duct. The radiologist considered that the descending duodenal diverticulum caused partial obstruction and dilation of the end of the common bile duct. Therefore, endoscopic ultrasonography (EUS) was conducted, and the findings suggested that the end of the common bile duct (CBD) had expanded and herniated (with a diameter of approximately 17.8 mm) into the duodenum, but the intrahepatic bile duct was not dilated. The duodenal papilla was located on the wall of the herniated intestinal cavity; after inflation, the herniated intestine returned to its normal position. Therefore, we contacted the radiologist to read the images again and ruled out the possibility of a descending duodenal diverticulum. Intraoperative exploration showed obvious biliary dilatation with a maximum diameter of 5 cm, and there were no stones or masses inside the common bile duct. Therefore, a choledochal cyst resection and Roux-en-Y hepaticojejunostomy were performed. The postoperative pathological diagnosis revealed chronic cholecystitis with mixed stones and adenomyosis; the common bile duct specimens were consistent with cysts. The patient recovered well after the operation, and was followed up for almost 2 years after discharge, and there were no obvious postoperative complications.