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Background  Hand, foot, and mouth disease (HFMD) is a common illness in young children. A monovalent vaccine has been developed in China protecting against enterovirus-71, bivalent vaccines preventing HFMD caused by two viruses are under development.    Objective  To predict and compare the incidence of HFMD under different vaccination scenarios in China.    Methods  We developed a compartmental model to capture enterovirus transmission and the natural history of HFMD in children aged 0–5, and calibrated to reported cases in the same age-group from 2015 to 2018. We compared the following vaccination scenarios: different combinations of monovalent and bivalent vaccine; a program of constant vaccination to that of pulse vaccination prior to seasonal outbreaks.    Results  We estimate 1,982,819, 2,258,846, 1,948,522 and 2,398,566 cases from 2015 to 2018. Increased coverage of monovalent vaccine from 0 to 80% is predicted to decrease the cases by 797,262 (49.1%). Use of bivalent vaccine at an 80% coverage level would decrease the cases by 828,560. Use of a 2.0× pulse vaccination for the bivalent vaccine in addition to 80% coverage would reduce cases by over one million. The estimated  R   0   for HFMD in 2015–2018 was 1.08, 1.10, 1.35 and 1.17.    Conclusions  Our results point to the benefit of bivalent vaccine and using a pulse vaccination in specific months over routine vaccination. Other ways to control HFMD include isolation of patients in the early stage of dissemination, more frequent hand-washing and ventilation, and better treatment options for patients.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12879-021-06157-w.

The burden of hand, foot, and mouth disease among children under different vaccination scenarios in China: a dynamic modelling study