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Objective: To determine the factors affecting the outcomes of percutaneous nephrolithotomy (PCNL) in patients in infantile/toddler and preschool age group. Materials and Methods: The data of 186 renal units from 152 patients who underwent PCNL were retrospectively analyzed. Patients under ≤72 months of age were included in the study. The patients were divided into two groups according to their age: infantile/toddler and preschool group. Demographics and stone features were compared between infantile/toddler and preschool age groups. Effects of different factors on complications and stone-free rates were investigated. Comparisons in the study were done using SPSS 24.0 software for Windows. Results: The mean age of the patients was 40.5 ± 16.5 months, and the female/male ratio was 87/99. The median stone burden was 1.92 cm ² (0.12–20). Stone-free rates were 75.3% and 84.4% when cases with Clinically Insignificant Residual Fragments were also included. The numbers of patients with Clavien grade 1, grade 2, and grade 3b complications were 7 (3.8%), 39 (21%), and 9 (4.8%), respectively. There was no difference between infantile/toddler and preschool children in terms of stone-free and complication rates ( p = 0.082, p = 0.088, respectively). Mini PCNL and tubeless—totally tubeless— urinary diversion techniques were more frequently performed in the infantile/toddler group compared to the preschool group ( p = 0.001, p = 0.028, respectively). Presence of staghorn stone was the only significant factor for complications, while the number of stones was significant for stone-free rates for patients ≤72 months ( p = 0.012, p = 0.001, respectively). Stone burden was the only predictive factor for complications in patients aged ≤36 months, while number of stones was predictive for success in patients aged between 37 and 72 months ( p = 0.034, p = 0.006, respectively). Conclusion: PCNL is a feasible and effective method in preschool age group with acceptable complications and high success rates. Presence of staghorn stone is predictive for complications, while number of stones is predictive for success in the preschool age group.