Background and Objective: The under-5 mortality rate is a commonly used indicator of population health and socioeconomic status worldwide. However, as in most resource-limited settings, deaths among children under-5 and in any age group in Ethiopia remain unreported. We aimed to systematically estimate neonatal, infant, and under-5 mortality trends, identify underlying causes, and make subnational (regional and chartered cities) between 1990 and 2019. Methods: We used the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD 2019) to estimate three key under-5 mortality indicators —the probability of death between the date of birth and 5 years (under-5 mortality rate, U5MR). The causes of death by age groups, sex, and year were estimated using Cause of Death Ensemble modelling (CODEm). Specifically, this involved a multi-stage process that includes a non-linear mixed-effects model, source bias correction, spatiotemporal smoothing, and a Gaussian process regression to synthesise mortality estimates by age, sex, location, and year. Results: In 2019, an estimated 190,173 (95% uncertainty interval 149,789–242,575) under-5 deaths occurred in Ethiopia, which was over two and a half times fewer 462,195 (427,639–499,980) than the deaths estimated for 1990. Nearly three-quarters (74%) of under-5 deaths in 2019 were within the first year of life, and over half (52%) in the first 28 days. The overall U5MR, IMR, and NMR in the country were estimated to be 52.4 (44.7–62.4), 41.5 (35.2–50.0), and 26.6 (22.6–31.5) deaths per 1000 livebirths, respectively, and differed substantially between regions. Conclusions: While all regional states in Ethiopia have experienced a decline in under-5, infant, and neonatal mortality rates in the past three decades, the rate of change was not large enough to meet globally agreed-upon Sustainable Development Goals (SDGs) targets. Inter-regional disparities also remain significant, with the biggest differences being in the neonatal period.