Iatrogenic bile duct injuries (BDIs) prevention during laparoscopic cholecystectomy (LC) relies on meticulous anatomical dissections through direct visualization. Near-infrared fluorescence (NIRF) with indocyanine green (ICG) improves the visualization of extrahepatic biliary structures. Although ICG can be administered either intravenously or intragallbladder, there remains uncertainty regarding the optimal method for different patient populations. This study sought to assess the suitability of each method for specific patient groups. Between October 2021 and May 2022, 59 consecutive patients underwent fluorescence-guided LC at West China Hospital of Sichuan University. Among them, 32 patients received an intravenous injection of ICG (10 mg) 10 to 12 hours prior to surgery (Group A: the intravenous group), while 27 patients received an intragallbladder injection of ICG (10 mg) (Group B: the intragallbladder group). Baseline clinical factors, inclusion criteria, and measurements of parameters and complications were assessed. Data were retrospectively collected and analyzed to evaluate the comparability of the two groups and the clinical outcomes. Groups A and B included 32 patients (18 males, 14 females), and 27 patients (13 men, 14 women), respectively. In our statistical analysis, significant differences were observed in preoperative diagnoses between the two groups (P=0.041), but the majority of other baseline clinical factors were comparable. Notably, no statistically significant differences were found in complication rates. However, Group A had a shorter operative time (60.38±9.35 vs. 66.78±9.88 min, P=0.01) and superior bile duct fluorescence (P=0.04) than Group B. Interestingly, fluorescence was not observed in impacted gallbladder stones in Group B. Additionally, patients with cirrhosis (P=0.008) and fatty liver (P=0.005) in Group B had higher common bile duct-to-liver ratios (BLRs) than those in Group A. ICG fluorescence cholangiography allows to visualize extrahepatic biliary anatomical structures with both administration methods. However, the efficacy of bile duct fluorescence varies with different administration routes in diverse patient populations. Hence, appropriate administration route selection for ICG should be tailored to individual patients.