Introduction: This study aims to investigate the effects of shock wave lithotripsy (SWL) treatment for proximal ureteral stones on the sexual functions of patients of both genders. Methods: In this prospective study, 30 female and 72 male patients who had received SWL treatment for proximal ureteral stones in our clinic between August 2019 and October 2020 were evaluated. CT, creatinine, urinary analysis, and culture were performed during the initial consultation for all patients. Information regarding the age, BMI, and stone burden of the patients was recorded. Male patients answered the International Index of Erectile Function-5 (IIEF-5) questionnaire, and female participants answered the Female Sexual Function Index (FSFI) 3 times: pre-procedural and post-procedural first and third month. CT was repeated on the first month, and any residues were noted. Results: The mean IIEF-5 scores of the male patients were 23.11 ± 8.11 prior to surgery, and it decreased to 19.74 ± 7.65 in the first month and 23.88 ± 9.23 in the third, p = 0.001. The mean FSFI scores of female patients were 18.2 ± 9.9, which decreased to 12.8 ± 6.12 in the first month and 17.8 ± 8.66 in the third, p = 0.001. Univariate analysis revealed that the patients’ age (male: p = 0.004 and female: p = 0.008) and BMI (male: p = 0.044 and female: p = 0.027) were related to the poorer scores for both genders. However, there were not any significant findings regarding stone burden (male: p = 0.054 and female: p = 0.078). Conclusions: The possibility of developing temporary sexual dysfunction should be taken into account for patients who are candidates for SWL treatment. As the patient’s age and BMI increase, SWL-related sexual dysfunction becomes more severe.