Near-infrared fluorescent cholangiography (NIRFC) is an emerging technique for easy intraoperative recognition of biliary anatomy. We present a case of cystic duct variation detected by NIRFC which had a potential risk for biliary injury if not detected. A 32-year-old female was admitted to the Seoul St. Mary's Hospital for surgery for an incidental gallbladder polyp. We performed laparoscopic cholecystectomy with NIRFC. In fluorescence mode, a long cystic duct and an accessory short hepatic duct joining to the cystic duct were found and the operation was completed safely. The patient recovered successfully. NIRFC is expected to be a promising procedure that will help minimize biliary injury during laparoscopic cholecystectomy.