This study aimed at evaluating territorial inequalities in avoidable mortality in children under 5 years of age in Colombia between 2000 and 2019.This was an ecological study.An ecological, longitudinal, multigroup study was conducted using secondary sources. Because of the hierarchical structure of the data, the effect of territorial characteristics on the count of avoidable under-five deaths was estimated using a three-level negative binomial regression model with random intercepts for municipality and fixed intercepts for time and departments.Between 2000 and 2019, there were 216,809 avoidable under-five deaths in Colombia (91.3% of all registered deaths of children under 5 years of age). A total of 1117 municipalities located in 33 departments were analyzed over five 4-year periods. Ecological relationships were found between avoidable under-five mortality and the percentage of adolescent births, female illiteracy, and multidimensional poverty at the municipal level (standardized mortality ratio: 1.43 95% confidence interval: 1.33-1.54 for the group with the highest level vs the group with the lowest level of poverty). Furthermore, multidimensional poverty was a confounding factor for the association between the percentage of the population living in rural areas and avoidable child mortality.Systematic and avoidable gaps were observed in mortality in children aged under 5 years in Colombia, where the territory constitutes an axis of inequality. Implementing strategies and programs that contribute to improving the conditions of women and socio-economic conditions in the territories should be a priority.