This study aims to comparatively analyse the importance and performance of the health of Korean and Japanese adolescents during the prolonged coronavirus disease 2019 (COVID-19) pandemic. Data were collected from 1,341 sampled Korean and Japanese adolescents in September 2021 through online and offline surveys. The collected data were analysed with frequency analysis, reliability testing, t-test, and importance-performance analysis (IPA). The following results were obtained. First, adolescents in the two countries perceive various factors about health as important during the COVID-19 pandemic, but their performance is weak compared to their perceived importance. Second, Korean adolescents had greater perceived importance for all factors of health perception compared to their Japanese counterparts. Third, the difference in performance between Korean and Japanese adolescents was especially evident for ‘hygiene management’, and there were significant differences in performance in ‘disease management’ and ‘physical activity’. Fourth, in quadrant 4 of the IPA matrix, there were similarities and differences in a particular factor of health perception between Korean and Japanese adolescents. Based on these results, we proposed measures to emphasise the importance of health and enhance performance among Korean and Japanese adolescents.