Objective Near-infrared fluorescence cholangiography (NIRF-C) can help to identify the bile duct during laparoscopic cholecystectomy. This retrospective study was performed to investigate the effect of NIRF-C in laparoscopic cholecystectomy. Methods Consecutive patients who underwent NIRF-C-assisted laparoscopic cholecystectomy (n = 34) or conventional laparoscopic cholecystectomy (n = 36) were enrolled in this study. Identification of biliary structures, the operation time, intraoperative blood loss, and postoperative complications were analyzed. Results Laparoscopic cholecystectomy was completed in all patients without conversion to laparotomy. The median operation time and intraoperative blood loss were not significantly different between the two groups. No intraoperative injuries or postoperative complications occurred in either group. In the NIRF-C group, the visualization rate of the cystic duct, common bile duct, and common hepatic duct prior to dissection was 91%, 79%, and 53%, respectively. The success rate of cholangiography was 100% in the NIRF-C group. NIRF-C was more effective for visualizing biliary structures in patients with a BMI of <25 than >25 kg/m2. Conclusions NIRF-C is a safe and effective technique that enables real-time identification of the biliary anatomy during laparoscopic cholecystectomy. NIRF-C helps to improve the efficiency of dissection.