Objective: We evaluate the discomfort and efficacy of instilling 2% lignocaine gel (Instillagel) versus smearing water-soluble gel (Aquagel) around the flexible cystoscope and external urethral meatus in men undergoing flexible cystoscopy for the first time and the overall efficacy of lignocaine gel in completion of the procedure. Materials and Methods: A total of 140 patients divided into two groups, were randomized for this study: group A (n = 70) received approximately 11 ml of 2% lignocaine gel (Instillagel) intraurethrally for approximately 15 min, while in group B (n = 70) approximately 10–15 ml of water-soluble gel (Aquagel) was smeared around the scope and external urethral meatus. Total completion time for each procedure was recorded. Primary outcomes were pain during instillation of lignocaine, during insertion of scope and cystoscopy. Pain was recorded by the patient using a 100-mm nongraphic rating visual analogue scale. Secondary outcome included procedure time and cost analysis. Results: The majority of patients in both groups reported mild pain with VAS 3 or less throughout the whole procedure. No significant difference was noted in the two groups at any stage of the procedure. Use of lignocaine gel added approximately 10 min to the procedure time. Conclusions: In our study there was no significant difference in patient discomfort between instilling lignocaine gel and smearing of Aquagel in completion of flexible cystoscopy. However, application of lignocaine gel added extra time, effort and cost to the procedure.