The swine-origin influenza A (H1N1) virus was responsible for the pandemic infection in 2009. We report a case of encephalitis diagnosed as the H1N1 virus infection in a young child. The H1N1 virus infection can be causative of the encephalitis, as with other influenza virus infections. For patients presenting with influenza-like illness accompanied by mental status changes or seizures, high suspicion for unusual presentations of influenza A virus infection and careful monitoring, including EEG and intracranial pressure monitoring, are essential for reducing complications.