A novel swine-origin influenza A (H1N1) virus was recently identified in Mexico. Some cases of infection with neurological complications have been reported to date. We report a case of acute necrotizing encephalopathy associated with the novel H1N1 virus in a 2-year-old European girl who suddenly developed fever, seizures, and altered mental status. Brain and spinal cord magnetic resonance imaging showed bilateral symmetrical lesions of the insulae, thalami, geniculate bodies, and pons tegmentum suggestive of an acute necrotizing encephalopathy. An involvement of meninges and spinal cord was observed configuring an acute necrotizing meningoencephalomyelitis.