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Purpose: To describe our experience in the use of percutaneous nephrolithotomy (PCNL) as a primary treatment for paediatric kidney stones and to highlight its benefits. Methods: The design was retrospective and observational. All the children treated for kidney stones from 2011 to 2021 were included. The population was divided into Group A (PCNL) and Group B (retrograde intrarenal surgery, RIRS). The outcomes were stone-free rate (SFR), the rate of procedures per patient, the rate of failure and the rate of complications. Results: Twenty-eight patients with 33 kidney units were included. Eighteen of them (64%) were males. The median age was 10 (IQR 6.8–13) years. Forty-seven procedures were performed. Twenty-four of them (51%) were mini-PCNL. Group A included 17 patients (61%). Group A presented a higher SFR (p = 0.007) and a lower number of procedures (p < 0.001). RIRS failed in five cases (45%) because of non-compliant ureter. Two urinary tract infections (UTI) were reported after PCNL and four UTIs after RIRS (p = 0.121). No major complications were reported. Conclusion: Mini-PCNL should be suggested as a primary approach for pediatric kidney stones. This technique presented a better effectiveness with a reduced number of procedures when compared to RIRS. [ABSTRACT FROM AUTHOR]