The healthy city approach toward addressing a variety of urban health challenges is increasingly important in the context of urbanization and globalization. For successful healthy city implementation and to help planners and decision makers as an initial step WHO introduced a tool, capacity mapping which aims to identify existing resources and assess capacity needs. Countries like Japan, Korea and Australia as well as some European and American countries have mapped their national capacity. However for specific cases like healthy cities, mapping capacity is rarely undertaken. Therefore, through a comparative study, this study maps the healthy city capacity in two selected countries: Indonesia and Korea, in order to assess comparative needs and improve healthy city development. Based on an extensive literature review and government documents, this study found that Indonesia and Korea have similarities in the historical development and national agenda of their healthy cities implementation but have differences in organizational structure, regulation and funding support. It appears that Indonesian national policy is stronger than Korean policy; Indonesia has joint regulation by the MOHA and the MOH which provide national guidelines for the healthy cities implementation while Korea only utilizes general guidelines. However in terms of funding availability, Korea’s healthy city program is stronger than that of Indonesia. Korea benefits from self-financing by each city, a membership fee from the KHCP and support from the Health Promotion Foundation while Indonesia has limited funding and no specific membership fee.