Background Due to a limited initial supply of COVID-19 vaccines, the prioritisation of individuals for vaccination is of utmost importance for public health . Here, we provide the optimal allocation strategy for COVID-19 vaccines according to age in Japan and South Korea . Methods Combining national case reports, age-specific contact matrices, and observed periods between each stages of infection (Susceptible-Exposed-Infectious-Quarantined), we constructed a compartmental model . We estimated the age-stratified probability of transmission given contact (q_i) using Bayesian inference method and simulated different vaccination scenarios to reduce either case numbers or death toll . We also performed sensitivity analyses on the proportion of asymptomatic cases and vaccine efficacy . Findings The model inferred age-stratified probability of transmission given contact (q_i) showed similar age-dependent increase in Japan and South Korea . Assuming the reported COVID-19 vaccine efficacy, our results indicate that Japan and South Korea need to prioritise individuals aged 20-35 years and individuals aged over 60 years, respectively, to minimise case numbers . To minimise the death toll, both countries need to prioritise individuals aged over 75 years . These trends were not changed by proportions of asymptomatic cases and varying vaccine efficacy on individuals under 20 years . Interpretation We presented the optimal vaccination strategy for Japan and South Korea . Comparing the results of these countries demonstrates that not only the effective contact rates containing q_i but also the age-demographics of current epidemic in Japan (dominance in 20s) and South Korea (dominant cases over 50s) affect vaccine allocation strategy.