Objectives This study aims to explore the association between women’s autonomy and skilled attendance during pregnancy and delivery in Nepal. Methods We adopt data from the Nepal Demographic and Health Survey (NDHS, 2011). We include only married women who gave birth in the 5 years preceding the survey (N = 4148). Women’s autonomy was assessed on the basis of four indicators of decision making: healthcare, visiting friends or relatives, household purchases and spending earned money. Each indicator was dichotomized (yes/no) and then summarized into a single variable to measure overall autonomy. Next, we measured health attendance (skilled vs. unskilled) during antenatal and delivery care. The association between women’s autonomy and skilled attendance was analysed using a logistic regression model. Results Most women had a medium (40 %) and high (35 %) level of overall autonomy. The proportion of women accessing skilled providers during antenatal and delivery care was 51 and 36 %. Women with autonomy in healthcare, visiting friends or relatives, making household purchases and spending money earned were associated with a higher likelihood of receiving care from skilled providers during antenatal care and delivery. An elevated probability of access to skilled attendance during antenatal (aOR 1.33; 95 % CI 1.10–1.59) and delivery care (aOR 1.38; 95 % CI 1.12–1.70) was reported among women with higher levels of overall autonomy. Conclusion Women’s autonomy was significantly associated with the maternal health care utilization by skilled attendants. This study will provide insights for policy makers to develop strategies in improving maternal health.