The aim of the study to compare low and intermediate shock wave frequency rates in terms of success and complications for treating pediatric kidney stones. This retrospective study was performed on 58 consecutive pediatric patients (24 girls, 34 boys) who underwent shock wave lithotripsy (SWL) for kidney stones with an electrohydraulic lithotripter between April 2014 and March 2016. In the first year, all children underwent SWL with a frequency of 90 SWs/min as an intermediate frequency (Group 90), and in the second year all children were treated by SWL using 60 SWs/min as a low frequency (Group 60). The mean age of the patients was 5.87 +/- 4.5 years. There were no significant differences in age, gender, stone characteristics and SWL energy level between the groups. Stone-free status was achieved in 14, 6 and 4 children in group 60; and in 10, 6 and 4 children in group 90 after one, two and three sessions, respectively. The stone-free rates were 80 and 74.1% after SWL and 90 and 88.9% after additional treatment in groups 60 and 90, respectively. The total median shock pulses were 2000 and 3600 in groups 60 and 90, respectively (p = 0.115). Efficiency quotients were 51.93 and 44.47 in groups 60 and 90, respectively. The mean total anesthesia times and complication rates did not differ between the groups. The low and intermediate frequency of SWL provided similar stone clearance in pediatric renal stones with similar anesthesia times. However, low SWL tended to need fewer shock pulses (2000/3600) for stone clearance, but the trend was not significant.