Malaria resulted in an estimated 627,000 deaths in 2020, the majority of which occurred in children under 5 years of age. Cerebral malaria (CM) is a severe manifestation of the disease with case fatality rates of up to 40%. Autopsies in children with CM have demonstrated sequestration of Plasmodium falciparum parasites in the brain as well as multiple other organs. Thus, multiple organ dysfunction syndrome (MODS) may be present in pediatric patients with CM, but its frequency and association with mortality have not been evaluated. This is a retrospective study of data collected prospectively from children with CM admitted in Blantyre, Malawi. Physical examination findings and laboratory values necessary to calculate a Pediatric Logistic Organ Dysfunction-2 (PELOD-2) score, a validated method that quantifies organ dysfunction in critically ill children, were abstracted. A total of 145 patients were included. Mortality was 15% (n = 22). Ten patients (7%) had single organ dysfunction, 36 (25%) had two organs involved, 68 (47%) had dysfunction of three organs, and 31 (21%) patients had four organs affected. Beyond neurologic dysfunction, other organ systems involved included hematologic (77%), renal (61%), cardiovascular (44%), and respiratory (1%). The median PELOD-2 score on admission was 4 (interquartile range [IQR] = 3-6) in survivors and 6.5 (IQR = 5-10) in the nonsurvivors (P < 0.0001). Admission PELOD-2 score predicted mortality with an area under the curve of 0.75. MODS is widespread in pediatric patients with CM. Objectively identifying children with MODS, and therefore at an increased risk of mortality, may allow for the allocation of limited resources.