A 65-year-old man presented with upper abdominal pain and was suspected of having choledocholithiasis. Endoscopic extraction of the stone was performed; however, a round filling defect in the common bile duct (CBD) persisted. Subsequent cholangioscopy showed the presence of a papillary tumor in the CBD, and the lesion was removed via the Whipple procedure. Microscopically, the papillary lesion was composed of pancreatic tissue in the submucosal layer of the CBD and therefore diagnosed as reflective of heterotopic pancreas. This is only the seventh case of heterotopic pancreas in the CBD reported in the English literature.