Double common bile duct is a rare congenital anomaly among biliary anomalies. The anomaly has an important clinical implication because of its association with biliary tract obstruction. In addition, if one of the two common bile ducts is mistaken for the cystic duct during surgery, residual stones and bile duct injury are likely to occur. Here, we report a case of double choledochal variation (Type Vb) with choledochal calculi. An 82-year-old woman was admitted to the hospital due to mild pain in the upper abdomen accompanied by vomiting for 3 days. Magnetic resonance imaging suggested common bile duct lithiasis, variation of the common bile duct and moderate biliary tract dilation. Laparoscopy combined with choledochoscopic lithotomy was performed for choledocholithotomy. During the operation, left and right choledocholithotomy was performed, and all the gallstones were removed via choledochoscope. The patient's post-operative recovery was good, and no recurrence of cholelith had been observed at the time of writing.