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A 62-year-old man underwent endoscopic mucosal resection for early gastric cancer. The follow-up computed tomography revealed biliary dilatation. The tumor was located in the lower bile duct with biliary dilatation, and no evidence of metastasis in other organs was noted. The patient underwent subtotal stomach-preserving pancreatoduodenectomy with pancreaticogastrostomy and Billroth I anastomosis. At 13 months after the operation, gastrointestinal endoscopy revealed a tumor lesion in the pancreaticogastrostomy site. Computed tomography revealed that the lesion was low enhanced in the pancreaticogastrostomy site and there was no evidence of other distant metastasis. Partial pancreatectomy was performed. Pathological findings of the tumor in the stump of the pancreas revealed findings similar to that of primary biliary carcinoma. Apparently, the patient was diagnosed with recurrence of bile duct cancer via the pancreatic duct. The patient underwent adjuvant chemotherapy for one year subsequent to partial pancreatectomy as the second operation. For 40 months after the second operation, there has been no evidence of recurrence of cancer.