Objective: This study was designed to compare the efficacy and safety of the supine and prone positions in percutaneous nephrolithotomies (PCNLs) used for the treatment of kidney stones in Indonesian patients. Methods: This was a single-blinded randomized controlled trial of those patients undergoing PCNLs from February to May of 2018. There were 19 subjects in the supine group and 19 in the prone group for a total of 38 study subjects. The study outcomes that were compared included the operative time, hospital length of stay (LOS), stone-free rate, blood loss, conversion to open surgery, blood transfusion, and complications. These outcomes were evaluated using the Student’s t test and the chi-squared test. Results: There were no significant differences in the patient demographics or stone locations between the two groups. Additionally, the medians of the operative times, LOSs, blood losses, and blood transfusions were not statistically different. There was a higher stone-free rate in the supine group than in the prone group (70.0% vs. 47.4%, respectively, p = 0.151). More subjects were transfused in the supine group (30.0%) than in the prone group (15.8%), but this difference was not statistically significant (p = 0.292). The only complications were infundibular lacerations, which occurred in 20% of the subjects in the supine group and 15.8% of the subjects in the prone group (p = 0.732). Conclusion: This study showed that the supine and prone positions for PCNLs had similar efficacy and safety outcomes.