Coxsackievirus A16 (CVA16) is one of the most prevalent enteroviral pathogens associated with hand, foot, and mouth disease. In the present study, we have investigated (1) whether the bioactive compound acetylshikonin (AS) inhibits CVA16 infection in vitro and in vivo and (2) the potential antiviral mechanism(s). The results suggest that AS is nontoxic at concentrations of up to 5 μmol/L and could directly inactivate virus particles at relatively low concentrations (0.08 μmol/L), thereby rendering CVA16 incapable of cellular entry. Correspondingly, the expression of viral RNA in vitro was also reduced 100-fold ( P < 0.05) when compared to infected, untreated controls. Results from a CVA16-infected neonatal mouse model indicate that, in comparison to the virus-infected, untreated group, body weights of the mice in the virus-infected, compound-treated group increased more steadily with less severe clinical symptoms. In addition, viral loads in internal organs significantly decreased in treated animals, concomitantly with both reduced pathology and diminished expression of the proinflammatory cytokines IFN-γ and IL-6. In conclusion, AS exerted an inhibitory effect on CVA16 infection in vitro and in vivo. Our study provides a basis for further investigations of AS-type compounds to develop therapeutics to mitigate CVA-associated disease in children.