Squamous cell carcinoma of the extrahepatic bile ducts is a very rare type of cancer with a virtually unknown pathogenesis. We present the case of a 66‐year‐old woman who underwent a pancreaticoduodenectomy with the postoperative diagnosis of squamous cell carcinoma of the common bile duct. Microscopically, the entire common bile duct showed squamous metaplasia. Besides, an invasive squamous cell carcinoma was found, stage pT3pN0. A next generation sequencing assay covering 315 tumor‐related genes revealed genomic alterations in seven genes: FBXW7, CREBBP, CTCF, FAT1, MAGI2, MLL2, and NOTCH1.