Enterovirus 71 (EV71) has emerged as a major cause of neurological threat in the world following the eradication of poliovirus. Most EV71 infections commonly result in hand-foot-mouth disease or herpangina, and some cases are associated with brainstem encephalitis and acute flaccid paralysis. Mortality was high in EV71 brainstem encephalitis complicated with pulmonary edema, particularly in children below 5 years of age. Destruction of vasomotor in the brainstem by EV71 produces autonomic nervous system dysregulation prior to the pulmonary edema. The pulmonary edema is the result of increased pulmonary vascular permeability caused by the direct brainstem lesions and/or a systemic inflammatory response syndrome produced by the release of cytokines and chemokines. There is currently no specific antiviral agent to treat or vaccine to prevent EV71 diseases. Treating severe EV71 brainstem encephalitis patients with intravenous IgG and milrinone is associated with significantly decreased mortality by attenuated sympathetic activity and cytokine production.