Choledocholithiasis means the presence of gallstone inside the common bile duct (CBD). Removing the bile duct stones can be done surgically using endoscopic catheters. In this study, we aim to assess the safety and efficacy of basket catheters compared to balloon catheters at bile duct stone clearance. We searched four databases for clinical trial and cohort studies that compare basket catheter and balloon catheter in bile duct stone extraction. We extracted data from the included studies. These data were pooled as mean difference (MD) or risk ratio (RR) with 95% confidence interval (CI) using Review Manager software (version 5.3) and OpenMetaAnalyst software for zero-event outcomes. In a total of 728 patients, we find that the balloon catheter was better than the basket catheter regarding incomplete bile duct stone clearance (RR = 0.91, 95% CI [0.85, 0.98], P = 0.01). Regarding the number of the extracted stones by both catchers, the analysis favored the balloon catheter over the basket for clearance when less than four stones (RR = 0.91, 95% CI [0.85, 0.99], P = 0.02) but no significant difference for more than four stones (RR = 0.77, 95% CI [0.48, 1.24], P = 0.29). There was no significant difference between the two groups. The analysis revealed that the balloon catheter is better than the basket catheter for choledocholithiasis regarding the complete clearance of the stone. However, there was no significant difference regarding the safety outcome.