Women’s autonomy in decision making has important sexual and reproductive health implications. This study uses a nationwide analysis in Nepal to examine women’s autonomy, attitude toward intimate partner violence (IPV) behaviors, and HIV-related knowledge in the execution of HIV protective behaviors such as having one sexual partner or getting an HIV test to prevent HIV transmission. Secondary data analysis was conducted using the nationally represented Nepal Demographic and Health Survey (2016–2021) dataset. The sample included 9,904 women ages 15 to 49 who self-identified as ever married. Factor analysis for women’s autonomy, attitude toward IPV behaviors, and HIV-related knowledge were conducted based on social dominance theory. Structural equation modeling was conducted, and the results indicated that higher autonomy decreased the risk of HIV infection through having one sexual partner. Factors related to multiple sex partners included unemployment, religious affiliation, and age. Similarly, higher autonomy, HIV-related knowledge, having a formal job, and urban residence increased women’s likelihood of taking an HIV test. Women’s higher education, greater wealth, religious affiliation, and youth also correlate with HIV testing. Future HIV prevention interventions should include strategies that support women’s social and economic empowerment and enhance women’s ability to make informed choices about their health and risks.