Minimally invasive percutaneous nephrolithotomy (mini-PCNL) and retrograde intrarenal surgery (RIRS) are both alternatives for PCNL to treat renal calculi. This study is aimed at comparing the stone-free rate (SFR) and other surgery parameters of two approaches for treating upper urinary calculi. We performed this meta-analysis in September 2016 by searching studies about mini-PCNL and RIRS for treating upper urinary calculi in various databases, and RevMan v.5.3 was applied. Three randomized controlled trials and ten nonrandomized trials were included, involving a total of 1317 patients. Meta-analysis showed that mini-PCNL group led to a higher SFR [odds ratio: 1.96; 95% confidence interval: 1.46-2.64;P < 0.00001] but brought a larger postoperative decrease in hemoglobin levels compared with RIRS. RIRS provided a shorter hospital time. There was no significant difference in operation time. Higher postoperative complications were detected in the mini-PCNL, but the difference was not significant. Grade I and III complications did not vary between two procedures, but grade II complications were of lower incidence in RIRS group. In the light of these results, compared with RIRS, mini-PCNL provided significantly higher SFR and efficiency quotient for managing calculi; however, it resulted in higher incidence of postoperative complications, larger hemoglobin drops, and longer hospital stay.