Accessibility of emergency medical care is one of the crucial factors in evaluating national primary medical care systems. While many studies have focused on this issue, there was a fundamental limit to the measurement of accessibility of emergency rooms, because the commonly used census-based population data are difficult to provide realistic information in terms of time and space. In this study, we evaluated the geographical accessibility of emergency rooms in South Korea by using dynamic population counts from mobile phone data. Such population counts were more accurate and up-to-date because they are obtained by aggregating the number of mobile phone users in a 50-by-50 m grid of a locational field, weighted by stay time. Considering both supply and demand of emergency rooms, the 2-step floating catchment analysis was implemented. As a result, urban areas, including the capital city Seoul, showed lower accessibility to emergency rooms, whereas rural areas recorded higher accessibility. This result was contrary to the results analyzed by us based on census-based population data: higher accessibility in urban areas and lower in rural. This implies that using solely census data for accessibility analysis could lead to certain errors, and adopting mobile-based population data would represent the real-world situations for solving problems of social inequity in primary medical care.