Enterovirus type 71 (EV71) is one of the main etiologic agents responsible for periodic epidemics of hand-foot-and-mouth disease (HFMD). The prevention and control of EV71 epidemics with effective anti-viral agents and vaccines is very important for public health. Because the pathogenesis of EV71 in the human body is not completely clear and genetic variations in the virus during its replication are difficult to control, we have focused on the development of an inactivated whole-virus vaccine. In this study, we screened 16 strains isolated from different areas of China and selected one strain for the development of an inactivated EV71 vaccine. The results of our study suggest that the FY-23K-B strain, which is a candidate strain for an EV71 inactivated vaccine, satisfied the requirements of vaccine production in terms of genetic stability, biological activity, and good immunogenicity. The experimentally inactivated vaccine produced using this strain was capable of inducing an immune response and offered protection to rhesus monkeys against future virus attacks.