Purpose: This study aimed to compare the current status of the national health insurance system (HIS) for advanced radiation technologies in Korea and Japan. Materials and methods: The data of the two nations were compared according to the 2019 guidelines on the application and methods of medical care benefit from the Ministry of Health and Welfare of Korea and the 2020 medical fee points list set by the Ministry of Health, Labor and Welfare of Japan. Results: Both countries have adopted the social insurance system and the general payment system which is fee-for-service for radiotherapy. However, for proton and carbon ion therapy, the Japanese system has adopted a bundled payment system. Copayment for radiotherapy is 5% in Korea and 30% (7–69 years old) in Japan, with a ceiling system. A noticeable difference is that additional charges for hypofractionation, tele-radiotherapy planning for an emergency, tumor motion-tracking, purchase price of an isotope purchase price, and image-guided radiotherapy are allowed for reimbursement in the Japanese system. There are some differences regarding the indication, qualification standards, and facility standards for intensity-modulated radiation therapy, stereotactic body radiation therapy, and proton therapy. Conclusion Patterns of cancer incidence, use of radiotherapy and infrastructure, and national HIS are very similar between Korea and Japan. However, there are some differences in health insurance management systems for advanced radiation technologies.