BackgroundsThe increasing prevalence of pediatric kidney stones worldwide makes minimally invasive lithotripsy like retrograde intrarenal surgery (RIRS) and percutaneous Nephrolithotomy (PCNL) more prevalent. However, their safety and efficacy are controversial. Consequently, a meta-analysis of the comparison between RIRS and PCNL is conducted.MethodsClinical trials were selected from PubMed, EMBASE, Scopus, and Cochrane Library databases. The data extraction and study quality assessment were performed by two individuals independently. The data relating to therapeutic effects were extracted and analyzed by Review manager 5.4.ResultsThirteen studies involving 1,019 patients were included. The micro-PCNL excelled in stone-free rate (P= 0.003), postoperative fever rate (P= 0.02), and Clavien–Dindo II complications (P= 0.05). Notably, the mean age of the micro-PCNL group was younger than other groups (P= 0.0005). The operation time in mini-PCNL was longer than RIRS (P< 0.00001) but with high heterogeneity (I2= 99%). There was no difference in Clavien–Dindo I, II, and III complications between the PCNL and the RIRS, but mini-PCNL showed a higher probability than RIRS in Clavien–Dindo I (P= 0.0008) and II complications (P= 0.007).ConclusionsCompared with RIRS, micro-PCNL could be a better therapeutic option for kidney stones in children. Of note, more parameters should be analyzed to illustrate the efficacy of different minimally invasive surgeries for pediatric kidney stones due to poor cases in our study.Systematic Review Registrationhttps://www.crd.york.ac.uk/prospero/#recordDetails, PROSPERO CRD42022323611