BACKGROUND The aim of this study was to assess the clinical outcomes of mini-percutaneous nephrolithotomy (Miniperc) and shock wave lithotripsy (SWL) for medium-sized renal stones. METHODS A literature search was performed in February 2020 using the Pubmed, Web of Science and Embase. The outcome measurements between two procedures were stone-free rates (SFR), complication rates, operative time, hospitalization stay time, re-treatment rate, auxiliary procedures rate and efficiency quotient. Results were pooled by Review Manager version 5.3 software. RESULTS Seven studies on 936 patients (N.=471 for SWL and N.=465 for Miniperc) were included. Miniperc was associated with a higher SFR (OR: 0.25; P<0.00001). In addition, we performed a subgroup analyses for pediatric renal stones and lower pole stones, pooled results also favored Miniperc for higher SFR. SWL was associated with higher auxiliary procedure (OR: 3.32; P<0.00001), higher re-treatment rate (OR: 19.19; P<0.00001) and lower EQ (OR: 0.18; P=0.0003) compared with Miniperc. Besides, SWL was associated with a lower complication rate (OR: 0.36; P=0.0001), shorter operative time (WMD: -34.01; P<0.00001), fluoroscopy time (WMD: -134.48; P<0.00001) and hospital time (WMD: -49.11; P<0.00001) compared with Miniperc. CONCLUSIONS Miniperc offers a significantly higher SFR, lower auxiliary procedure and re-treatment rate, but SWL was associated with fewer complications.