Purpose Shock wave lithotripsy (SWL) is the first option in the treatment of pediatric kidney stones; however, optimal frequency is still uncertain. The aim of this study was to compare low frequency [60 shocks per minute (SWs/min)] and intermediate frequency [90 SWs/min] in terms of lithotripsy success, complications, cardiac arrhythmia, anesthesia time, secondary procedures, and efficiency quotient (EQ) in children. Methods Seventy-eight consecutive children who received SWL for radiopaque renal stones between July 2016 and January 2020 were randomly divided into two groups: Group 60 (SWL frequency: 60 SWs/min) and Group 90 (SWL frequency: 90 SWs/min). After exclusion (remaining 71 children), Group 60 (n = 38) and Group 90 (n = 33) were compared using univariate analysis. Results The median age of children (37 girls, 34 boys) was 5 (1-16) years. Patient demographics and stone features were similar between the groups. Success rate after the last SWL session was 81.6% (n = 31) for Group 60 and 87.9% (n = 29) for Group 90 (p = 0.527). Stone-free rate after the first, second, and third sessions was 42.1%, 18.4%, and 21.1% for Group 60 and 48.5%, 27.3%, and 12.1% for Group 90, respectively. Additional treatment rate was similar between the groups. In Group 60, the EQ was 57.83, and it was 64.07 in Group 90. Median total anesthesia time was significantly longer in Group 60 (74.5 min) than in Group 90 (32 min; p < 0.001). Conclusion Intermediate frequency and low-frequency pediatric SWL have similar success rates; however, intermediate-frequency SWL has a shorter anesthesia time.