Women with greater autonomy have higher HIV-related knowledge and condom use. Inability to negotiate safer sex in high-risk situations might increase HIV infection. This study examined the relationship between women's autonomy and ability to negotiate safer sex practices among married women. The 2011 Nepal Demographic and Health Survey data were used. The data were collected by two-stage stratified cluster sampling and face-to-face interviews. Autonomy was measured in Decision-Making Participation and Assets Ownership, while ability to negotiate safer sex consists of Refusal of Sex and Ask for Condom Use. Among 12,674 women of 15–49 years, married women were analyzed (n = 8,896). Women with greater autonomy in decision-making participation were more likely to negotiate safer sex. After controlling for socio-demographic factors, odds ratios (OR) for refusal of sex was 2.70 (95% CI [2.14, 3.40]) in women with the highest decision-making participation. These women showed higher OR for ‘ask for condom use’ in high risk situations (2.10, 95% CI [1.81, 2.44]). Assets ownership also demonstrated a positive statistical relationship with asking for a condom use (OR 1.31, 95% CI [1.10, 1.56]). The results point to the importance of women's autonomy on sexual health. It emphasizes women's empowerment-based approach to curbing HIV/AIDS in developing countries.