Purpose Cystoscopy procedures can cause distress among patients. Patient perspectives on health services are essential inputs in decision-making. This study investigated the patient preferences in Spain regarding single-use cystoscopes (SUC) compared to reusable cystoscopes and their willingness to pay (WTP) for cystoscopy procedures. Patients and Methods Between May and June 2021, an anonymous survey was distributed to Spanish patients who had previously undergone a cystoscopy. The survey included patient preference measures on reusable cystoscopes compared to SUCs and a discrete choice experiment. The survey was distributed through a human data science company (IQVIA), collected using an online survey tool (QuestionPro ® ), and analyzed using Stata/MP, StataCorp. Results Of 300 respondents, 148 (49.33%) were female and 150 (50%) were male, and mainly between 18–49 years (247, 82.33%). Most (265, 88%) preferred to have their procedure performed with a SUC rather than a reusable cystoscope. Among these patients, 215 (80%) could imagine asking their doctor to use a SUC. A total of 231 (77%) respondents indicated an increased level of concern about the risk of exposure to contamination related to their cystoscopy following the COVID-19 pandemic. Patients would pay 62 EUR to have their initial consultation and cystoscopy procedure on the same day (p < 0.001), 59 EUR to reduce the environmental impact, and 57 EUR to reduce the risk of contamination (p < 0.001). Conclusion Patients prefer to undergo cystoscopy using an SUC on the same day as their initial consultation. The increased contamination concerns due to the COVID-19 pandemic and WTP to reduce the risk of cystoscope contamination may explain patients’ preferences for SUCs. The most important attributes related to their cystoscopy procedure are the ability to have their procedure performed on the same day as their initial consultation, the reduction of the environmental impact, and the reduction of the contamination risk.