Infection with enterovirus (EV) 71 is usually associated with hand-foot-and-mouth disease and herpangina. The most frequent neurologic complication is brainstem encephalitis. A 30-month-old boy visited the pediatric emergency department with fever, lethargy, and abnormal eye contact. His mental status was slightly drowsy. On hospitalization day 2, the patient experienced respiratory arrest with apnea. Brain magnetic resonance imaging revealed bilateral symmetric T2-high signal lesions without enhancement in the posterior aspect of the brainstem and left medial temporal lobe. Electroencephalography was indicative of diffuse cerebral dysfunction with diffuse high amplitude and irregular delta activities. He underwent a gene study and was diagnosed with myoclonic epilepsy with ragged red fibers syndrome. We report a case of EV 71 brainstem encephalitis by polymerase chain reaction for nasopharyngeal aspirates and feces with rapid progression within one day of fever without the manifestation of throat and skin lesions because of his underlying mitochondrial disease.