In this study, we aimed to determine factors affecting the success rate of percutaneous nephrolithotomy (PNL) in children. The series consisted of 41 consecutive children operated on by the same surgical team for renal calculi with PNL between June 2002 and May 2015 in our institution. A single calyx or pelvic stone was described as simple, while calculi located in more than one location (calyx and pelvis or more than one calices) or staghorn stones were described as complex. The procedure was deemed successful if the patient was completely stone-free (SF) or had residual fragments <4 mm. Thirty-four patients were found to be SF or had residual fragments <4 mm on the postoperative first day, thus the success rate was 82.9%. In complex stones, the success rate was significantly lower (45.5%) than simple stones (96.7%) (p < 0.001). The grade of hydronephrosis (Grade 0-1 vs. Grade 2-3) also had a negative impact on the success, with rates of 92.6% vs. 64.3%, respectively (p = 0.022). Previous urological procedure history on the same side yielded a success rate of 58.3%, whereas the success rate in the primary patients was 93.1% (p < 0.001). The localization of the stone (complex vs. simple), degree of hydronephrosis, and history of previous urological procedures were found to be the factors that affected the success of the paediatric PNL.