Background: Urolithiasis is a common, sever, painful, and costly disease with a high probability of relapse. This study was performed to compare the effect of Polycitra-K containing potassium citrate and Bicitra containing sodium citrate in the treatment of kidney stones in children who referred to Hazrat Masoumeh hospital in Qom. Methods: This double-blind randomized clinical trial study was carried out on 176 patients aged between 5 and 18 years old with kidney stones, hypocitraturia, and negative urine who referred to Hazrat Masoumeh hospital in Qom (Iran). Patients were divided into 2 groups of treatment (a dose of 1 mL/kg or 1-1.5 mg/ kg Polycitra-K) and control (Bicitra in the same dose). The results of kidney ureter bladder X ray (KUB ) was followed and the 2 groups were compared. The chi-square test or the Fisher exact test was used to analyze qualitative values in the treated groups. Results: Regarding bladder stones, there was a significant difference between the 2 treatment groups (p = 0.025), in which16 patients (18.2%) in the Polycitrat-K group and 29 patients (33%) in the Bicitra group had bladder stones. With respect to stone passage, 58 patients (65.9%) in the Polycitra-K group and 36 patients (40.9%) in the Bicitra group were recorded. Conclusion: Oral Polycitrat-K is an effective preferential supplement against kidney stones in children due to urine alkalization, but the results of our study showed that both Polycitrat-K and Bicitra drugs have similar effects as therapeutic agents. Registration code in the Iranian Registry of Clinical Trials: IRCT20190619043945N1