Abstract Objective To analyze the clinical features of children with hand foot and mouth disease (HFMD) who died. Methods 331 deaths due to HFMD between 2010 and 2014 were included in this retrospective study; 15 autopsies were performed. Results Most deaths were seen in children aged below 3 y, and with enterovirus 71 infection (91%). The mean (SD) duration of HFMD from onset to death was 3.7(2.9) d. The mean (SD) age of fast progressors (from onset to death less than 4 days) was 17.4 (9.2) mo. Most of them were diagnosed as stage 3 and stage 4 of HFMD. Various pathological changes were observed in brain after autopsy, especially in brain stem and medulla. Conclusions The brain stem encephalitis with the neurotropism of enteroviruses seems to be the main contributor to the death in HFMD.