Background: The safety and feasibility of percutaneous nephrolithotomy (PCNL) compared with retrograde intrarenal surgery (RIRS) are debated. This systematic evaluation was performed to obtain comprehensive evidence with regard to the treatment outcomes of PCNL compared with RIRS for management of renal stones in patients with solitary kidney. Methods: A systematic search of Medline, Embase, Pubmed, and the Cochrane Library was performed to identify studies that compared PCNL with RIRS. Outcomes of interest included perioperative variables, complications, and stone-free rate (SFR). Results: 4 studies assessing PCNL vs. RIRS were included for meta-analysis. Although patients underwent PCNL have higher initial SFR than RIRS (OR: 3.72, 95% CI:2.38 to 5.83; P＜0.001), patients underwent RIRS have less intraoperative blood loss (dropped Hb: WMD= 3.49 g/L, 95% CI:2.83 to 4.15; P＜0.001), lower blood transfusion rates (OR= 5.31, 95% CI:1.36 to 20.68; P=0.02), and higher incidence rate of steinstrasse (OR:0.20, 95% CI:0.04 to 0.91; P=0.04). All the other calculated results including operation time (WMD: -9.87 minute, 95% CI:-30.11 to 10.37; P=0.34), final SFR (OR:1.65, 95% CI:0.80 to 3.42;P=0.18) and overall complications (OR:1.22, 95% CI:0.78 to 1.93; P=0.38) are similar between the two groups. Conclusions: Our results indicate that PCNL has higher initial SFR than RIRS in the treatment of renal stones in patients with a solitary kidney; the overall complications were comparable in both groups. However, RIRS, with less blood loss and transfusion rate, may be an alternative in selected patients.