Background Endourological procedures are widely used to treat benign urinary disorders and the double-J stent is routinely used. However, its potential impact on sexual function remains unclear. Therefore, we performed a quantitative systematic review to determine the relationship between endourological procedures with or without double-J stent and post-operative sexual function. Methods We conducted a search of PubMed, EMBASE, Web of Science, and Cochrane Library databases up to December 2018 for studies that compared sexual function before and after endourological procedures. The quality of the included studies was evaluated using the Risk Of Bias In Non-randomized Studies of Interventions (ROBINS-I). We performed subgroup analyses to explore heterogeneity. A random effects model was used to combine the results. Results Five prospective studies involving 485 sexually active participants were identified. Pooled results showed that, in patients without a double-J stent, the change in sexual function after endourological procedures was not significant in men (mean difference [MD]: - 0.61, 95% confidence interval [CI]: - 1.43 to 0.22, p = 0.148) or women (MD: 0.53, 95% CI: - 0.52 to 1.57, p = 0.322). However, in patients with indwelling double-J stent, sexual function scores significantly declined after the procedure in both men (MD: -4.25, 95% CI: - 6.20 to - 2.30, p < 0.001) and women (MD: -7.17, 95% CI: - 7.88 to - 6.47, p < 0.001). Conclusions Our meta-analysis suggests that indwelling double-J stent after endourological procedures could be a crucial factor causing temporary sexual dysfunction post-operatively. Our results may be used to provide evidence-based advice to patients.