Background The Percutaneous nephrolithotomy (PCNL) is an endourological method applied as the standard or tubeless method for kidney stones treatment. Material and Methods In a retrospective study, 88 surgery units involving 75 children up to 18 years old with kidney stones who underwent the surgery for 8 years with one of the two methods of standard or tubeless PCNL were evaluated and compared considering the success rate of operation, hemoglobin, and hematocrit drop, medications, transfusion, duration of surgery and the length of hospital stay. Results Among the 88 patients, 47 cases were operated with the standard PCNL and 41 cases by tubeless method. In children whom operated by standard and tubeless PCNL, the complete success rate of operation was 87.2% and 100% (P = 0.006), the need for blood transfusion was 2.1% and 0% (P = 1.00), the need for opioids was 27.7% and 14.6% (P = 0.134), the decrease in hemoglobin was -1.82±0.94 and -1.30±0.98 mg/dl (P = 0.024), the decrease in hematocrit was -5.40±2.66 and -3.52 ± 3.11 mg/dL (P = 0.003), mean surgery duration was 109.30±53.27 and 101.46±31.92 minutes (P = 0.414), the duration of postoperative hospitalization was 3.38±1.76 and 2.46±1.27 days (P = 0.007) and the frequency of fever was 23.4% and 7.3% (P = 0.04), respectively. Conclusion The success rate of kidney stone surgery in children with the tubeless PCNL is higher than the standard method, and its complications are lower.