Background: Childhood stunting is a major challenge to the growth and development of nations by affecting millions of children across the world. Although Ethiopia has made steady progress in reducing stunting, the prevalence of stunting is still one of the highest in the world. This study aims to investigate the spatial variation and factors associated with childhood stunting in Ethiopia.Methods: This study is a secondary data analysis of the 2019 Ethiopian Mini Demographic and Health Survey (EMDHS). A total of 4,971 children aged 0–59 months were included in the analysis. The Getis-Ord statistics tool has been used to identify areas with high and low hotspots of stunting. A multilevel logistic regression model was used to identify factors associated with stunting.Results: The prevalence of stunting was found to be 36.86% in Ethiopian under-five children. Statistically significant hotspots of stunting were found in northern parts of Ethiopia. Both individual and community-level factors determined the odds childhood stunting among under-five children. Children in the age group between 24–35 months were more likely to be stunted than children whose age was less than one year [AOR = 3.74; 95 % CI: (3.04–4.59)]. Children with mothers who had completed higher education had lower odds of being stunted compared to children whose mothers had no formal education [AOR = 0.55; 95%CI: (0.38–0.82)]. Children from the poorest wealth quintile had higher odds of being stunted compared to children from the richest wealth quintiles [AOR = 2; 95 % CI: (1.46–2.73)]. Children living in Tigray (AOR =3.64; 95 % CI: 2.17–6.11), Afar (AOR 2.02; 95 % CI 1.19-3.39), Amhara (AOR =2.29; 95 % CI: 1.37–3.86), Benishangul Gumz (AOR=1.87; 95% CI: 1.10-3.17) and Harari (AOR=1.95; 95% CI: 1.17-3.25) regions were more likely to be stunted compared to children living in Addis Ababa.Conclusion: This study showed that both individual and community-level factors were significant predictors of childhood stunting. Improving maternal education, improving the economic status of households, improving age-specific child feeding practice, and providing additional resources to regions with high hotspots of childhood stunting are recommended.