Background: Few studies have examined the performance of the public long-term care insurance (LTCI) from the perspective of geographic equity. This study investigated regional variations and associated factors in the supply and utilization of nursing home care within and also between Japan and Korea. Methods: A comparative dataset was developed by extracting data from 2013–2015 LTCI statistics yearbooks and Organization for Economic Cooperation and Development regional statistics, as well as other comparable data in Japan and Korea. The unit of analysis was the prefecture in Japan and the province in Korea. We computed variation indices and conducted regression analyses for regional variations within each country and decomposition analyses to examine the variations between the countries. Results: The overall regional supply and use of nursing home care were higher in Japan, but the regional variations in Korea were larger than in Japan. In both countries, the nursing home supply was negatively associated with the proportion of older people with independent living. Nursing home use was also negatively associated with the supply of hospital beds and home care agencies in Korea; the relationship was the opposite in Japan, however. The country-based differences were more likely to be explained by differences in the distributions of the variables included in the analytical model than country-specific characteristics. Conclusion Regional-level nursing home supply and use were unequal in both countries, and the contributing factors were not the same. Policy efforts are needed to advance regional equality in long-term care (LTC) and collaboration between health and LTC institutions for frail older people, especially in Korea.