Abstract Purpose Female sexual function can be influenced by many somatic and psychosocial factors. Many chronic diseases, such as irritable bowel syndrome (IBS), can induce long-term suffering leading to a negative effect on sexual function. The impact of IBS on women’s sexual health is an underexplored area, particularly in Middle Eastern populations. The aim of this study is to compare the prevalence and domains of sexual dysfunction in Jordanian women with and without IBS. Patients and Methods This is a cross-sectional study, conducted at two hospitals in Jordan, from February to August 2024. 504 women, aged 18 or more, agreed to participate in this study, including 279 diagnosed with IBS. Our questionnaire incorporated clinical and sociodemographic data, relevant items of the Rome IV criteria, and the validated Arabic version of the Female Sexual Function Index (FSFI). Results Among 504 female participants (mean age 34.1 ± 10.7 years), 88.2% were found to have sexual dysfunction, defined as an FSFI score <26.55, in the IBS group, and 76% in the non-IBS group, with an odds ratio of 2.354 (p <0.001). IBS patients demonstrated significantly lower mean scores in most FSFI domains (desire, arousal, lubrication, orgasm, and satisfaction) and a lower total FSFI score (19.2 ± 9.9 vs 16.6 ± 10.2; p < 0.05 for all comparisons), while the pain domain did not differ significantly between the two groups. Logistic regression identified IBS as a statistically significant predictor of sexual dysfunction (p = 0.007). Conclusion IBS is associated with a higher prevalence of female sexual dysfunction in Jordan, which was demonstrated by lower scores in most sexual function domains. Our findings emphasize the need to integrate sexual health assessment as a part of IBS care. Future studies should explore the causality and the mechanism of this relationship.