Introduction: Antiretroviral therapy (ART) for HIV/AIDS is associated with adverse events (AEs). However, little is known about the differences in the risk of AEs between women and men living with HIV/AIDS. This study aims to determine (1) whether there are sex differences in the risk of AEs in people with HIV/AIDS treated with ART and (2) the prevalence of AEs to the reproductive system and bone mineral density in women. Methods and analysis: This systematic review (SR) will include randomised trials evaluating ART in people living with HIV/AIDS with at least 12 weeks of duration follow-up. Searches will be conducted in Medline, Embase, Cochrane Library, Epistemonikos, Lilacs, trial registries and grey literature databases, without restriction on publication status, year of publication and language. The primary outcome will be the risk of ART discontinuation or drop-outs/withdrawals of ART due to AEs and the number of any treatment-emergent AE. The secondary outcomes are the incidence of serious clinic or laboratory (grade 3 and/or 4) treatment-emergent AEs, hospitalisation, death and AEs specific to the reproductive system and bone mineral density (osteoporosis, osteopenia and fractures) of women. Selection, data extraction and quality assessment will be performed by pairs of reviewers. Cochrane collaboration tools will be used to assess the risk of bias. If appropriate, a meta-analysis will be conducted to synthesise results. The overall quality of the evidence for each outcome will be determined by the Grades of Recommendation, Assessment, Development and Evaluation. Ethics and dissemination: The results of this SR will assist the formulation of public policies aimed at the management and monitoring of AEs of ART in people living with HIV/AIDS. A deliberative dialogue will be scheduled with the Department of Chronic Conditions and Sexually Transmitted Infections of Brazil’s Ministry of Health to align the project with policymakers’ interests.