Most autoimmune diseases (AIDs) during childhood debut with more severe and aggressive forms, with life-threatening conditions that increase the need for intensive care therapy. This study describes the clinical, laboratory, and health outcome features of pediatric patients with AIDs admitted to the pediatric intensive care unit (PICU). This is a retrospective cross-sectional study that included the clinical records of all pediatric patients with AIDs admitted to the PICU between 2011 and 2020 in Cali, Colombia. In total, 225 PICU admissions from 136 patients were evaluated. Median age was 13 (11–15) years, and the median disease duration was 15 (5–38.5) months. Systemic lupus erythematosus was the most prevalent disease (91, 66.9%), followed by vasculitis (27, 19.8%). The leading cause of PICU admission was AID activity (95, 44.3%). C-reactive-protein levels were associated with infections (p <0.0394). Mortality occurred in 12 (8.8%) patients secondary to AID activity, primarily, diffuse alveolar hemorrhage (6, 50%). A longer disease duration was associated with mortality (p <0.00398). AID activity was the leading cause of PICU admission and mortality. Pulse steroid therapy, mechanical ventilation, and inotropic and vasopressor support were associated with nonsurvival.