Introduction: Women’s decision-making autonomy has a positive effect on the scale-up of contraceptive use. In Ethiopia, evidence regarding women’s decision-making autonomy on contraceptive use and associated factors is limited and inconclusive. Therefore, this study was intended to assess married women’s decision-making autonomy on contraceptive use and associated factors in Ethiopia using a multilevel logistic regression model. Methods: The study used data from the 2016 Ethiopia Demographic and Health Survey that comprised of a weighted sample of 3668 married reproductive age women (15–49 years) currently using contraceptives. A multilevel logistic regression model was fitted to identify factors affecting married women’s decision-making autonomy on contraceptive use. Akaike’s information criterion was used to select the best-fitted model. Results: Overall, 21.6% (95% confidence interval = 20.3%–22.9%) of women had decision-making autonomy on contraceptive use. Community exposure to family planning messages (adjusted odds ratio = 2.22, 95% confidence interval = 1.67–3.05), media exposure (adjusted odds ratio = 2.13, 95% confidence interval = 1.52–3.23), age from 35 to 49 years (adjusted odds ratio = 2.09, 95% confidence interval = 1.36–4.69), living in the richer households (adjusted odds ratio = 1.67, 95% confidence interval = 1.32–3.11), and visiting health facility (adjusted odds ratio = 2.01, 95% confidence interval = 1.34–3.87) were positively associated with women’s decision-making autonomy on contraceptive use. On the contrary, being Muslim (adjusted odds ratio = 0.53, 95% confidence interval = 0.29–0.95), being married before the age of 18 years (adjusted odds ratio = 0.33, 95% confidence interval = 0.12–0.92), and residing in rural residence (adjusted odds ratio = 0.48, 95% confidence interval = 0.23–0.87) were negatively associated with women’s independent decision on contraceptive use. Conclusion: Less than one-fourth of married reproductive age women in Ethiopia had the decision-making autonomy on contraceptive use. Media exposure, women’s age, household wealth, religion, age at marriage, visiting health facilities, community exposure to family planning messages, and residence were the factors associated with women’s decision-making autonomy on contraceptive use. The government should promote women’s autonomy on contraceptive use as an essential component of sexual and reproductive health rights through mass media, with particular attention for adolescent women, women living in households with poor wealth, and those residing in rural settings.