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We performed a systematic review and meta-analysis comparing stone-free rates between retrograde intrarenal surgery (RIRS) and percutaneous nephrolithotomy (PCNL), using updated, more reliable evidence.Randomized controlled trials comparing RIRS and PCNL for >2 cm stones were identified from electronic databases. Stone-free rates for the procedures were compared by qualitative and quantitative syntheses (meta-analyses). Outcome variables are shown as risk ratios (RRs) with 95% confidence intervals (CIs).Eleven articles were included in this study. Most recently published studies exhibited relatively low quality during quality assessment. For the meta-analysis comparing success (stone-free) rates between PCNL and RIRS, the forest plot using the random-effects model showed an RR of 1.11 (95% CI 1.02–1.21, P < .014) favoring PCNL. After determining the among-study heterogeneity, subgroup analysis was performed of 9 studies with less heterogeneity: the stone-free rate of PCNL was superior to that of RIRS using a fixed-effect model (RR 1.07, 95% CI 1.01–1.14, P < .019) for these studies.RIRS can be a safe and effective procedure for selected patients with large renal stones. However, in this meta-analysis, the postoperative stone-free rate of PCNL was higher than that of RIRS in patients with >2 cm renal stones.