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Background Despite numerous national and international efforts to alleviate child growth faltering, it remains a global health challenge. There is a growing body of literature that recognizes the importance of women’s empowerment in a wide range of public health topics, such as the utilization of maternal healthcare services, agricultural productivity, and child nutrition. However, in Ethiopia, the relationship between women’s empowerment and child nutritional status is not studied at the national level. This study aimed to determine the association between women’s empowerment and growth faltering in under-5 children in Ethiopia. Methods The data source for this analysis is the 2016 Ethiopian Demographic and Health Survey (EDHS): a nationally representative household survey on healthcare. The EDHS employed a two-stage stratified cluster sampling technique. We computed standard women’s empowerment indices, following the Survey-based Women’s emPowERment index approach. A multilevel logistic regression model that accounted for cluster-level random effects was used to estimate the association between women’s empowerment and child growth faltering (stunting, wasting and underweight). Results Attitude to violence, social independence, and decision-making were the three domains of women’s empowerment that were associated with child growth faltering. One standard deviation increase in each domain of empowerment was associated with a reduction in the odds of stunting: attitude towards violence (AOR = 0.92; 95% CI 0.88–0.96; p p = 0.049), and decision-making (AOR = 0.93; 95% CI 0.87–0.99; p = 0.023). Similarly, each standard deviation increase in attitude towards violence (AOR = 0.93; 95% CI 0.89–0.98; p = 0.008), social independence (AOR = 0.91; 95% CI 0.86–0.97; p = 0.002), and decision-making (AOR = 0.92; 95% CI 0.86–0.99; p = 0.020) were associated with a decrease in the odds of having underweight child. Conclusions Ensuring women’s empowerment both in the household and in the community could have the potential to decrease stunting and underweight in a rapidly developing country like Ethiopia. Policymakers and health professionals need to consider women’s empowerment in this unique context to improve nutritional outcomes for children and alleviate growth faltering.