Background In the last years, Colombia has improved most of the mayor health indicators, however, some inequalities –as those related with child health– remain over time; understanding the historical behavior of health inequalities, allows to evidence structural and persistent social inequalities that explain these trends. This study aims to describe territorial inequalities in child health among departments and municipalities of Colombia between 2000 and 2018, throughout the analysis of trajectories of under-five avoidable mortality rate. Methods We carried out a longitudinal and multi-group ecological study. We analyzed the longitudinal dynamics of avoidable mortality of Colombian under-five children by applying group-based trajectory approach and taking the Colombian departments and municipalities over time as analysis units. Results We included all the 33 departments and 1 118 municipalities in 19 years. The avoidable mortality rate in under-five children (AMRC) in the first and last year of follow-up was 23.3 and 12.2 deaths per thousand live births (lb), respectively. We identified three different trajectories of avoidable mortality at the department level: a best (57.6%; AMRC: 20.7–10.5 per thousand lb), moderate (30.3%; AMRC: 31.9–15.9) and worst trajectory (12.1%; AMRC: 56.4 − 26.9). We described the common characteristics of the departments within each identified group. At the municipality level we found five different trajectories, the worst had the greater reduction, but it was not enough to close the gap. We also found different trajectories when amenable, preventable, and mixed avoidable under-five mortality were analyzed among departments and municipalities. Conclusions The gaps in avoidable child mortality among departments and municipalities in Colombia have been reduced, however, territorial disparities persist over time, mainly in amenable mortality through timely and quality medical care. Those trajectories express inequities in child survival originated from the socioeconomic, political and health system determinants in Colombian territories.