Percutaneous Nephrolithotomy (PCNL) and Retrograde Intrarenal Surgery (RIRS) are widely used in the management of kidney stones. But the safety and efficiency between these two technologies is still a mystery. This meta-analysis was performed to compare the efficacy as well as safety of Minimally Invasive Percutaneous Procedures (MIPPs) including ultra mini-PCNL, mini-PCNL, and micro-PCNL with RIRS. PubMed, Embase and Scopus were searched, and twelve studies included data on 1207 cases (613 for MIPPs and 594 for RIRS) satisfied the inclusion criteria and were included in this research finally. MIPPs were found to be associated with higher stone-free rate but longer hospital stays, and a larger drop in hemoglobin levels. Difference between MIPPs and RIRS in complication rate, operative time, and total cost were not notable. Given no obvious difference in the complication rate and higher efficacy, our findings suggest that mini-PCNL should be recommended over RIRS for stones>2 cm, and that for stones<2 cm any of MIPPs or RIRS are reasonable.