Purpose: Kidney stones are one of the most common urological problems. When deciding on the method of treatment for this common disease, the cost of the procedure should also be taken into consideration. Materials and methods: We performed a retrospective analysis of 55 patients who underwent percutaneous nephrolithotomy and 75 patients who underwent retrograde intrarenal surgery between January 2016 and November 2018. Until operative success was achieved, all additional surgical procedures, extracorporeal shock wave lithotripsy procedures, and interventional procedures required to resolve complications were recorded. Total cost was compared between the percutaneous nephrolithotomy and retrograde intrarenal surgery groups. Results: No significant difference was found between the percutaneous nephrolithotomy and retrograde intrarenal surgery groups in terms of gender, mean age, stone side, stone localization and stone surface area. The total cost of 55 patients that underwent percutaneous nephrolithotomy was calculated as US$14.766 after the first operation, and the total cost of 75 patients that underwent retrograde intrarenal surgery was determined to be US$46.627. The mean cost per patient was calculated US$320 +/- US$186 for percutaneous nephrolithotomy and US$749 +/- US$242 for retrograde intrarenal surgery (p < 0.001). Conclusions: Percutaneous nephrolithotomy is a lower-cost and successful method in the surgical treatment of 1-3 cm stones, but the serious complications involved in this operation should be kept in mind.