The epidemiology of the coronavirus disease (COVID-19) has been scarcely described in individuals under 18 years old, particularly during the first months of the pandemic. The study aimed to describe the COVID-19 epidemiology in the Colombian department of Bolívar from March 2020 to April 2021 among individuals under 18 years. Furthermore, we explored whether the use of data generated by a Bolívar reference laboratory captures the departmental epidemiology. Two information sources were used; the national COVID-19 surveillance system and the Bolívar COVID-19 reference laboratory. In using a population-based ecological approach and information from confirmed symptomatic cases, epidemic curves and heat maps were constructed to assess the COVID-19 dynamics and patterns by sex, age, and residence (Cartagena vs. 45 other municipalities). The COVID-19 incidence was comparable between males and females but varied by age group, being higher in children aged 10 years and older. Cartagena had a significantly higher number of cases and experienced early epidemic peaks. Our analyses suggest that information generated by the reference laboratory does not capture the COVID-19 departmental epidemiology, despite conducting population-based surveillance across Bolívar. The study provides a retrospective characterization of the COVID-19 epidemiology in an understudied population and information that may be useful for future evidence-based responses.