This study aimed to compare the safety and efficacy of laser lithotripsy and pneumatic lithotripsy, the two most commonly used transurethral lithotripsy methods for treating bladder stones in children in Iraq. Between January 2013 and December 2016, 64 children with bladder stones were included in this prospective randomized study, after ethical committee approval and written consent from the children’s parents or caregivers were obtained. Patients were assigned randomly by computer software to two groups treated with either pneumatic cystolithotripsy or laser lithotripsy. A 9 Fr. semirigid ureteroscope was used to pass the lithotripter through and fragment the stone. A catheter of 8–12 Fr. was then introduced and kept in place for 24 h. All children were hospitalized for 24 h, and the catheter was removed the next morning. Outpatient follow-up was maintained for 6–12 months. In terms of operation outcomes and complications, the laser lithotripsy group had a significantly longer duration of operation (74.5 ± 26.6 min vs. 51.5 ± 17.2 min, p = 0.001), whereas the number of patients requiring an extended hospital stay was significantly higher in the pneumatic lithotripsy group (48.5% vs. 16.1%, p = 0.006). Moreover, pneumatic lithotripsy was associated with a significantly greater risk of having at least one adverse effect (64% greater than that in the laser group). Stone clearance rates did not significantly differ between treatment groups. In conclusion, both pneumatic and laser lithotripters can be used to treat children with bladder stones with high efficacy and safety.