Empirical knowledge suggests that acute neurologic disorders are common in sub-Saharan Africa, but studies examining the true burden of these diseases in children are scarce. We performed this prospective, observational study to evaluate the prevalence, clinical characteristics, treatment approaches, and outcomes of children suffering acute neurologic illness or injury (ANI) in an urban and rural site in the Democratic Republic of the Congo. Over 12 months, 471 out of 6,563 children admitted met diagnostic criteria for ANI, giving a hospital-based prevalence of 72/1,000 admissions. Two hundred and seventy-two children had clinical findings consistent with central nervous system infection but lacked complete diagnostic evaluation for definitive classification. Another 151 children were confirmed to have cerebral malaria (N = 109, 23% of admissions), bacterial meningitis (N = 38, 8% of admissions), tuberculous meningitis (N = 3, 0.6% of admissions), or herpes encephalitis (N = 1, 0.21% of admissions). Febrile convulsions, traumatic brain injury, and epilepsy contributed less significantly to overall hospital prevalence of ANI (3.19/1,000, 1.37/1,000, and 1.06/1,000, respectively). Overall mortality for the cohort was 21% (97/471). Neurologic sequelae were seen in another 31% of participants, with only 45% completing the study with a normal neurologic examination. This type of data is imperative to help plan effective strategies for illness and injury prevention and control, and to allow optimal use of limited resources in terms of provision of acute care and rehabilitation for these children.