To estimate the prevalence of Juvenile Idiophatic Arthritis (JIA) in Colombia. This cross-sectional study identified patients with a diagnosis code for AIJ (ICD-10 M08-M09) using a nationally-representative database of health care resource utilization provided by the “Sistema Integral de Información de la Protección Social (SISPRO)” in 2017. In addition, estimated prevalence was contrasted using data of personal history of JIA using a database of patients with ≤ 16 years affiliated to a subsidized-regime insurance company (N = 397,160) of the Caribbean region of Colombia. The estimated prevalences were extrapolated to the overall Colombian population using the demographic projections of individuals with ≤ 16 years of age (14,588,845) provided by the Departamento Administrativo Nacional de Estadisticas (DANE). In 2017, the prevalence of JIA in the subsidized-regime company was 13 per 100,000 (52/397.160). According to the data of SISPRO the prevalence of JIA in Colombia was 10.9 per 100,000 (1,602/14,588,845). Extrapolating these estimations to the general population of Colombia, the estimated number of prevalent cases of JIA in Colombia could be approximately 1.602 and 1.896 cases, respectively. These estimations are lower in Colombia compared to previously reported prevalence globally (between 60 and 400 cases per 100,000).