A 66-year-old Japanese woman was admitted to our hospital with upper right quadrant pain and jaundice. Laboratory data indicated the presence of obstructive jaundice. A diagnosis of cholecystocholedo-cholithiasis was made by ultrasonography. Endoscopic retrograde cholangiography revealed choledochal stones with septum formation in a portion of the common hepatic duct up to where an anomalous bile duct drained from the caudate lobe of the liver. We performed a cholecystectomy, T-tube drainage, and partial resection of the septum when these findings were confirmed at surgery. Histological examination of the removed septum showed fibrous stroma under atrophic mucosa. To our knowledge, this is the eighteenth reported case in Japan of septum formation of the bile duct. However, no other such case to date has been seen combined with an anomalous hepatic duct of the caudate lobe of the liver. Selective cholangiography by choledochoscope and computed tomography with a thin guide-wire inserted to the bile duct were useful in confirming the origin of the anomalous bile duct. This case may serve as further evidence of the assumption that septum formation of the common (hepatic) bile duct is a malformation of congenital origin.