<b><i>Background:</i></b> Advances in micro-percutaneous nephrolithotomy (PCNL) for kidney stones have made it an alternative approach to the retrograde intrarenal surgery (RIRS) approach. Nevertheless, the superiority of micro-PCNL over RIRS is still under debate. The results are controversial. <b><i>Objectives:</i></b> The purpose of this study was to systematically evaluate the clinical results in patients presenting with kidney stones treated with micro-PCNL or RIRS. <b><i>Methods:</i></b> A literature search was done for electronic databases to identify researches that compared micro-PCNL and RIRS till December 2019. The clinical outcome included complications, stone-free rates (SFRs), hemoglobin reduction, length of hospital stay, and operative time. <b><i>Results:</i></b> Five articles were included in our study. The pooled results revealed no statistical difference in the rate of complications (OR = 0.99, 95% CI = 0.57–1.74, <i>p</i> = 0.99), length of hospital stay (MD = −0.29, 95% CI = −0.82 to 0.24, <i>p</i> = 0.28), and operative time (MD = −6.63, 95% CI = −27.34 to 14.08, <i>p</i> = 0.53) between the 2 groups. However, significant difference was present in hemoglobin reduction (MD = −0.43, 95% CI = −0.55 to 0.30, <i>p</i> < 0.001) and the SFRs (OR = 0.59, 95% CI = 0.36–0.98, <i>p</i> = 0.04) when comparing RIRS with micro-PCNL. <b><i>Conclusions:</i></b> Compared with micro-PCNL to treat kidney stones, RIRS is associated with better stone clearance and bearing higher hemoglobin loss. As the advantages of both technologies have been shown in some fields, the continuation of well-designed clinical trials may be necessary.