Purpose The aim was to compare laparoscopic pyelolithotomy and percutaneous nephrolithotomy in terms of efficacy and safety for the treatment of renal pelvis stones larger than 2.5 cm in pediatric patients.Methods Our study consisted of two groups. Group 1 included 33 patients who underwent laparoscopic pyelolithotomy (LPL) between January 2013 and March 2022, and group 2 included 39 patients who underwent percutaneous nephrolithotomy (PCNL). The basic clinical parameters of the patients were recorded. Mean operation time, stone size, estimated blood loss, blood transfusion rate, postoperative hospital stay, stone-free rate, postoperative analgesia requirements, intraoperative complications, and early and late postoperative complications were compared between the two groups.Results In our study, the mean age of the patients in groups 1 and 2 was 8.89 +/- 1.58 years and 9.1 +/- 1.85 years, respectively (p = 0.657). The mean stone size was 2.37 +/- 0.38 cm in group 1 and 2.55 +/- 0.45 cm in group 2 (p = 0.64). The mean operation time was 85.65 +/- 20.55 min in group 1, while it was 76.11 +/- 13.12 min in group 2 (p = 0.08). The stone-free rate was 100% in both groups. Intraoperative mean blood loss, need for postoperative analgesia, blood transfusion and intraoperative complication rates were significantly higher in the PCNL group (p < 0.01, p = 0.02, p < 0.01, p < 0.01, respectively).Conclusion Our results show that laparoscopic pyelolithotomy is a safe and effective method for pediatric patients with large kidney stones.