Background The distribution of under-five mortality (U5M) worldwide is uneven and the burden is higher in Sub-Saharan African countries, which account for more than 53% of the global under-five mortality. In Ethiopia, though U5M decreased substantially between 1990 and 2019, it remains excessively high and unevenly distributed. Therefore, this study aimed to assess geographic variation and factors associated with under-five mortality (U5M) in Ethiopia. Methods We sourced data from the most recent nationally representative 2019 Ethiopian Mini-Demographic and Health Survey for this study. A sample size of 5,695 total births was considered. Descriptive, analytical analysis and spatial analysis were conducted using STATA version 16. Both multilevel and spatial analyses were employed to ascertain the factors associated with U5M in Ethiopia. Results The U5M was 5.9% with a 95% CI 5.4% to 6.6%. Based on the multivariable multilevel logistic regression model results, the following characteristics were associated with under-five mortality: family size (AOR = 0.92, 95% CI: 0.84,0.99), number of under-five children in the family (AOR = 0.17, 95% CI: 0.14, 0.21), multiple birth (AOR = 14.4, 95% CI: 8.5, 24.3), children who were breastfed for less than 6 months (AOR = 5.04, 95% CI: 3.81, 6.67), people whose main roof is palm (AOR = 0.57, 95% CI: 0.34, 0.96), under-five children who are the sixth or more child to be born (AOR = 2.46, 95% CI: 1.49, 4.06), institutional delivery (AOR = 0.57, 95% CI: 0.41, 0.81), resident of Somali and Afar region (AOR = 3.46, 95% CI: 1.58, 7.55) and (AOR = 2.54, 95% CI: 1.10, 5.85), respectively. Spatial analysis revealed that hot spot areas of under-five mortality were located in the Dire Dawa and Somali regions. Conclusion Under-five mortality in Ethiopia is high and unacceptable when compared to the 2030 sustainable development target, which aims for 25 per 1000 live births. Breastfeeding for less than 6 months, twin births, institutional delivery and high-risk areas of under-five mortality (Somali and Dire Dawa) are modifiable risk factors. Therefore, maternal and community education on the advantages of breastfeeding and institutional delivery is highly recommended. Women who deliver twins should be given special attention. An effective strategy should be designed for intervention in under-five mortality hot spot areas such as Somali and Dire Dawa.