This research compares the level of media literacy, social stigma, and the correlation between media literacy and social stigma in Indonesia and Japan, in order to know the right measures to eliminate the social stigma, as one of the inequality that occured in the pandemic. The research question proposed in this study include: 1) Media literacy correlation with social stigma towards the infected person, 2) The severerity of social stigma towards the infected person, and 3) How to solve the social stigma caused by social media in times of the current digital society. In the era of pandemic, people are not only fear the disease, but also the social stigma it brings. With that in mind, we would like to see whether or not the media literacy have any significance towards the occurence of the social stigma. In this research, we found that people with low media literacy have a bigger chance to have a high social stigma towards the person with COVID-19. The result of this research could also be implemented in the government polocy making to prevent the ostracization of a certain group related to COVID-19.