A man in his 70s came to our department with jaundice. He was diagnosed with Merkel cell carcinoma in the left eyebrow area 3 years ago and was followed up after tumor resection. Endoscopic retrograde cholangiopancreatography was performed because the computed tomography and abdominal ultrasonography revealed bile duct dilatation. However, the duodenum was too narrow and deformed to reach the ventral papilla. Percutaneous transhepatic cholangiodrainage was performed, and bile cytology revealed no malignant findings; however, it did not sufficiently reduce the jaundice. Subsequently, endoscopic ultrasound-fine needle biopsy was performed on his right adrenal mass, which led to a diagnosis of the rare Merkel cell carcinoma. In summary, we report here of a case in which endoscopic ultrasound-fine needle biopsy led to the diagnosis of Merkel cell carcinoma recurrence.