To assess the use of miniaturized percutaneous nephrolithotomy (mini-PCNL) for renal stones in children, as well as its safety and efficacy. Seventy-seven patients with more than 15 mm renal stones whose age was less than 15 years were enrolled in this prospective case-controlled study at Al-Ramadi Teaching Hospital, Ar Razi Private Hospital, and Ghazi Al-Hariri Hospital for Surgical Specialties, Anbar and Baghdad, Iraq. The study was conducted from January 2020 to January 2024. The group mentioned above served as group A, and it was compared to the control group (group B), which consisted of 70 adult patients aged 18–60 years. Patients in both groups underwent mini-PCNL. Gender, stone size and location, time of operation, stone-free rate, hemoglobin drop, need for blood transfusion, postoperative fever, associated visceral injury, and need for further interventions such as extracorporeal shock wave lithotripsy or flexible ureteroscopy (ESWL or FURS) were compared in both groups. The age of patients in group A ranged from 8 months to 15 years with a mean (4.30 ± 3.16), while in group B ranged from 18 to 60 years with a mean (36.3 ± 12.0), p-value 0.001. There were no statistically significant differences regarding gender distribution, stone size, and location, p-value > 0.05. The stone-free rate was 87.01% for group A and 88.57% for group B, with no statistical difference, p-value 0.773. Hemoglobin drop was 1.096 ± 0.412 for group A and 1.195 ± 0.110 for group B, p-value 0.046. Blood transfusion was needed in one case in each group with no statistical difference, p-value 0.946. The need for ESWL was 3 cases in group A, and 2 cases in group B, with no statistical difference between the two groups, p-value 0.729. The need for FURS was 4 cases in group A and 3 cases in group B, p-value 0.796. Operative time was 30 to 125 min in group A and 34 to 129 min in group B, p-value 0.941. Postoperative fever was seen in 23 cases in group A and 21 cases in group B, p-value 0.986. Minor liver injury was seen was seen in one case in each group. The use of mini-PCNL for treating renal stones in children is safe and effective as it is associated with a relatively low rate of significant complications and achieves a high stone-free rate.