Background This study aimed to assess whether urethral pain can be alleviated by urination in male patients undergoing flexible cystoscopy. Methods Ninety-six male outpatients undergoing flexible cystoscopy were randomly divided into two groups. Patients in the test group urinated during flexible cystoscopy, whilst patients in the control group received no instructions to do so. All patients received 10 mL of 2% lidocaine gel prior to assessment. Using 0 (no-pain) to 10 (unbearable severe pain) pain scores (VAS), we assessed patient discomfort prior to anesthesia gel perfusion (baseline), during gel perfusion, during cystoscope insertion through the urethra, and 15 min post-examination analysis. The entire protocol was completed by a single doctor in our Department of Urology. Results The groups showed no statistical differences regarding age or examination time. During cystoscope insertion, the test group recorded significantly lower pain scores 2 (IQR 1-3) - compared to the control group 3 (IQR 2-3), (P = 0.001). No significant differences between other evaluation points were observed between groups. Conclusion Urethral pain can be significantly alleviated by urination in male patients undergoing flexible cystoscopy through the urethra.