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Objectives: To determine the effect of intravesical onabotulinum toxin‐A (BoNT‐A) treatment on sexual functions in female patients with refractory interstitial cystitis/bladder pain syndrome (IC/BPS). Methods: Female patients with IC/BPS refractory to previous treatments were included in the study between January 2020 and April 2022. Patients were treated with the trigone‐sparing injection (Group 1) or trigone‐included injection (Group 2) techniques. 100 Units of BoNT‐A was applied submucosally on 20 different points. The patients were evaluated with visual analog scale (VAS), O'Leary‐Sant Interstitial Cystitis Symptom Index (ICSI), Interstitial Cystitis Problem Index (ICPI), Female Sexual Function Index (FSFI) questionnaires, 3‐day voiding diary, uroflowmetry, and post‐voiding residual volume analysis in the preoperative period, as well as on the 30th and 90th days postoperatively. For the repeated measurements, analysis of variance was used to assess the time‐dependent variation across groups. Results: The baseline FSFI score of the patients was 15.96 ± 3.82. Following the treatment, the FSFI scores were 22.43 ± 4.93 and 24.41 ± 5.94 on the 30th and 90th days, respectively (p <.001). We observed statistically significant improvement in all FSFI subdomains (p <.05). Statistically significant improvements with treatment on ICSI, ICPI, and VAS scores were achieved (p <.05). Preoperative FSFI scores were similar in Group 1 and Group 2 (p =.147). While the preoperative FSFI scores were 17.00 ± 3.73 and 14.84 ± 3.72 for Group 1 and Group 2, respectively, the scores after the treatment were 22.85 ± 5.01 and 21.98 ± 5.01 on the 30th day, and 24.62 ± 6.06 and 24.19 ± 6.05 on the 90th day postoperatively. Significant improvement was observed in FSFI scores with treatment, and no difference was observed between the two groups in terms of treatment response (p =.706). Conclusions: Intravesical BoNT‐A injection in the treatment of women with refractory IC/BPS improves sexual functions. It also significantly improves pain and symptom scores. Both trigone‐sparing and trigone‐including injections are similarly safe and effective. [ABSTRACT FROM AUTHOR]