Very limited data are available exploring the potential influence of gender on Retrograde Intrarenal Surgery outcomes. This study investigates the gender-specific influence of ShuoTongureteroscopy (ST-urs) and Flexible Ureteroscopy (F-urs) surgeries on operation efficacy and patient recovery in a sample of the Somali population. We enrolled 390 participants. Participants were stratified into four gender-specific subgroups based on ureteroscopy operation type: 27.7% males in S-urs (group1), 44.4% females in S-urs (group2), 18.7% males in F-urs (group3), and 9.2% females in F-urs (group4). Primary outcomes included operation time, postoperative hospital stay duration, and VAS Pain Score. Multivariate logistic regression was used to assess associations. The mean age was 29.53 ± 7.61 years, 72.1% male and 27.9% female, with 46.4% of the patients undergoing ST-urs and 53.6% undergoing F-urs. Women had higher odds of prolonged hospital stays (OR = 2.62, 95% CI: 1.43-4.82, p < 0.001) and post-operation pain (OR = 5.06, 95% CI: 2.95-8.68, p = 0.002). Among men who underwent F-urs procedure, there was a significantly higher odds ratio (OR) of 6.14 (95% CI: 2.86-13.19, p < 0.001) for experiencing a long operation time. Conversely, for females, those who underwent S-urs surgery had a notably lower OR of 0.32 (95% CI: 0.13-0.79, p = 0.013) for long operation time, whereas those who underwent F-urs surgery exhibited a substantially elevated OR of 5.36 (95% CI: 1.85-15.53, p < 0.001). Both females undergoing F-urs surgery (OR: 5.16, 95% CI: 2.61-10.21, p < 0.001) and those undergoing F-urs surgery (OR: 5.25, 95% CI: 2.17-12.73, p < 0.001) experienced significantly higher post-operative pain. Our research reveals gender disparities in retrograde intrarenal surgery outcomes. Women experience longer hospital stays and higher postoperative pain levels compared to men. F-urs procedures are associated with longer operation times and hospital stays, particularly affecting women. Contrarily, ST-urs offers shorter operation times for women but leads to prolonged hospital stays and heightened postoperative pain.