Background: Previous studies have suggested that when intimate partner violence (IPV) tends to be persistent across a woman’s life span, her newborn offspring have a higher risk of ill health and mortality. There is a high prevalence of both IPV and neonatal mortality in Ethiopia, but the issue of IPV has remained largely outside the focus of child survival programs in this country. One of the noticeable reasons is a lack of evidence regarding the effect of IPV on neonatal mortality. Therefore, this study investigated the effect of maternal IPV on neonatal mortality in Ethiopia. Method: This study used nationally representative data from the 2016 Ethiopian Demographic and Health Survey. A total of 2,863 currently married women of reproductive age who gave birth in the preceding 5 years were included in analysis. Regression models using propensity scores were used. Results: The prevalence of physical, emotional, and sexual IPV were 24.5%, 22.9%, and 12.0%, respectively. About 56% of women had also experienced at least one act of partner controlling behavior. Maternal IPV experience (a composite measure of physical, sexual, and emotional abuse) was associated with increased neonatal mortality (adjusted odds ratio [AOR] = 2.58, 95% confidence interval [CI] = [1.03, 6.45]). In addition, the odds of neonatal mortality were 2.75 times (AOR = 2.75; 95% CI = [1.05, 7.2]) higher among women who had experienced three or more partner controlling behaviors than women who had experienced less than three or none. Conclusion and implication: Maternal IPV is significantly associated with risk of neonatal mortality in Ethiopia. There is a clear need for IPV interventions in child survival programs. Therefore, existing neonatal survival strategies should focus beyond the direct causes of neonatal mortality, and they need to target IPV as an underlying factor to neonatal morbidities and mortality.