Influenza has been associated with neurological complications. We describe the case of a toddler who presented with symptoms and signs of acute encephalopathy and hydrocephalus. Neuroimaging demonstrated cerebral edema and multifocal diffusion restriction in the thalamus and splenium of the corpus callosum. Influenza A was detected from the nasopharyngeal aspirate. The final diagnosis was acute influenza-associated encephalopathy. Despite treatment with a neuraminidase inhibitor and intravenous immune globulin, the toddler developed neurological sequelae. This case highlights a rare but severe complication of influenza in young children and the importance of influenza vaccination.