Introduction Sexual dysfunction in women with HIV is a necessary but understudied aspect of HIV complications in women living with HIV. This study reports the prevalence, pattern, and risk factors for sexual dysfunction in women living with HIV in southwest Nigeria. Methods A validated Female Sexual Function Index was used to determine sexual dysfunction in a cross-sectional study design involving 2926 adult women living with HIV in a large, publicly funded tertiary HIV treatment centre in Lagos, Nigeria. A score of less than 26.5 indicated sexual dysfunction. Multivariate logistic regression analysis was performed to identify risk factors for sexual dysfunction. P<0.05 was considered statistically significant at a 95% confidence interval (CI). Results The prevalence of sexual dysfunction was 71.4%. The types of dysfunctions detected included disorder of desire (76.8%), sexual arousal (66.0%), orgasm (50.0%), pain (47.2%), lubrication (47.2%), and satisfaction (38.8%). Multivariate analysis showed that menopause (aOR: 2.0; 1.4 – 4.1), PHQ score of 10 and above (aOR: 2.3; 1.7 – 3.2), co-morbid medical conditions (aOR: 1.8; 1.4 – 2.7), use of protease inhibitor-based antiretroviral therapy (aOR: 1.3; 1.2 - 2.1) and non-disclosure of HIV status (aOR: 0.7; 0.6-0.8) were factors associated with sexual dysfunction. Conclusions Sexual dysfunction is common among Nigerian women living with HIV. Menopause, use of protease inhibitor-based regimens, PHQ score of at least 10, co-morbid medical condition, and non-disclosure of HIV status were associated with sexual dysfunction. National HIV programmes, in addition to incorporating screening and management of sexual dysfunction in the guidelines, should sensitise and train health workers on the detection and treatment of sexual dysfunction.