We report a case of small pancreatic carcinoma misdiagnosed as superficially spreading cholangiocarcinoma using percutaneous transhepatic cholangioscopy (PTCS). The patient was a 72-year-old man admitted to a local hospital with obstructive jaundice. The patient underwent percutaneous transhepatic biliary drainage and PTCS. He was referred to our hospital with a diagnosis of superficially spreading cholangiocarcinoma. Cholangiography revealed a stenosis of the common bile duct, and also revealed some irregularities from the common hepatic duct to the left hepatic duct, suggesting a superficial spread of cancer. No pancreatic tumor was identified by endoscopic retrograde pancreatography or by enhanced computed tomography. Cholangioscopy disclosed an elevated tumor with torsional vessels and granular mucosal lesions, which were extended to the left hepatic duct. Repeated cholangioscopic biopsies of the bile duct mucosa revealed adenocarcinoma. The patient was diagnosed with superficially spreading cholangiocarcinoma extending to the left hepatic duct and the right anterior hepatic duct. Left trisectionectomy combined with pancreatoduodenectomy was performed. The cut surface of the resected specimen showed a pancreatic head tumor that was 8 mm in diameter. Histological findings of the resected specimen revealed adenocarcinoma arising from the pancreatic head with invasion in the common bile duct. Additionally, extensive inflammatory granulation tissue was observed along the surface of the bile duct, without any evidence of carcinoma. This case implies to us that the results of PTCS, even after repeated biopsies, should be interpreted with great caution.