Hand, foot and mouth disease (HFMD) is a common acute infectious disease caused by enteroviruses, whose most common pathogens are human enterovirus 71 and coxsackievirus A16. Coxsackievirus A6 is relatively rare. Here a rare HFMD case complicated with systemic herpes and cervical spinal cord involved is reported. The rashes caused by HFMD were most commonly seen at the palm of hand and foot, hip, knee and elbow joint. The infant was developed to systemic herpes quickly and complicated with significantly increased neuron specific enolase and imaging changes of cervical spinal cord in magnetic resonance imaging (MRI). Under the treatment of anti-inflammatory, anti-virus, and supporting therapy, the systemic herpes disappeared and the infant fully recovered. Clinical physicians should paid more attention to this rare case caused by coxsackievirus A6.