Hand, foot and mouth disease is a common acute viral infectious disease that poses a serious threat to the life and health of young children. With the development of an effective inactivated EV71 vaccine, CA16 has become the main pathogen causing HFMD. Effective and safe vaccines against this disease are urgently needed. In our previous study, a bivalent inactivated vaccine was shown to have good immunogenicity and to induce neutralizing antibodies in mice and monkeys. Repeated administration toxicity is a critical safety test in the preclinical evaluation of vaccines. In this study, BALB/c mice were used to evaluate the toxicity of the bivalent vaccine after multiple intradermal administrations. Clinical observation was performed daily, and body weight, food intake, hematological characteristics, serum biochemical parameters, antinuclear antibodies, CD4+/CD8a+ T-cell proportions, bone marrow smear results and pathology results were recorded. The results showed that there was no significant change at the injection site and no adverse reactions related to the vaccine. The bivalent inactivated EV71-CA16 vaccine exhibits good safety in mice, and these results provide a sufficient basis for further clinical trials.