Mini-PCNL is one of the most effective surgical methods in the treatment of kidney stones in pediatric patients. In this study, we aimed to compare PCNL in the supine–prone position in pediatric patients (especially operation time, postop complications, hospital stay and stone-free rates).We conducted our study in a randomized and prospective manner. Patients with lower pole stones larger than 1 cm, stones larger than 1.5 cm in the pelvis, upper pole, midpole or multiple locations, and patients who did not respond to ESWL or whose family that preferred mini-PCNL to be the primary treatment were included in the study. Patients with any previous kidney stone surgery, patients with coagulation disorders and patients with retrorenal colon were excluded from the study. Between 2021 and 2023, a total of 144 patients underwent PCNL. 68 of these patients had supine PCNL and 76 prone PCNL. Postoperative Clavien grade1 complication occurred in a total of 7 patients in the prone position; Clavien grade1 complication occurred in 1 patient in the supine position. The mean operation time for prone PCNL was 119.88 ± 28.32 min, and the mean operative time for supine PCNL was 98.12 ± 14.97 the mean hospitalization time in prone PCNL was 3.56 ± 1.12 days, and 3.00 ± 0.85 days in supine PCNL. In conclusion, supine PCNL is a safe and effective method in the treatment of pediatric kidney stones and postoperative complications were observed to be less; the operation time and hospital stay were shorter in supine PCNL.