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Abstract Introduction Percutaneous nephrolithotomy (PCNL) is widely performed as the preferred treatment for kidney stones larger than 20 mm in pediatric patients, with current research focusing on comparing outcomes between prone and supine positions to determine optimal procedural positioning. Therefore, the aim of this study is to compare the efficacy of prone versus supine positioning in pediatric PCNL, providing clarity on this critical aspect of the procedure to guide clinical decision-making. Methods We conducted a systematic review in PubMed, Embase, Scopus, Cochrane, Web of Science and Google Scholar. We included studies that compared PCNL in prone vs supine positions for pediatric patients. Our primary outcome was stone-free rate (SFR). Secondary outcomes included operative time, length of hospital stay and overall complications rate. The statistical analysis was performed using Review Manager 5.4. Results We retrieved 8 articles, with 269 patients in the prone group and 223 patients in the supine group. The mean age of all patients was 7.92 years old. Our findings presented no statistically significant difference in SFR between the two positions (OR 0.67; CI95 0.38, 1.18; p = 0.17; I2 = 0%). Additionally, we noted a significant reduction in operative time in the supine position group (MD 13.75; CI95 4.35, 23.15; p = 0.004; I2 = 84%). At the same time, the length of hospital stay after the procedure was lower in supine group (MD 0.61; CI95 0.34, 0.88; p |