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Background: This study compares and analyzes the importance and performance of Korean and Japanese adolescents’ health awareness in the long COVID-19 pandemic situation. Methods: A frequency analysis was conducted on data collected from 1341 Korean and Japanese adolescents in September 2021 through online and offline surveys to confirm their characteristics (reliability was verified through Cronbach’s α). A paired sample test was conducted to analyze health awareness differences and performance of each variable between Korean and Japanese middle-school students and between male and female participants, substantiated by importance-performance analysis (IPA). Results: First, Korean adolescents perceived importance for all factors of health perception greater as compared to their Japanese counterparts. Second, performance differences between Korean and Japanese adolescents were especially significant in hygiene management, disease management and physical activity. Third, in Quadrant 4 of the IPA matrix, there were similarities and differences in a particular factor of health perception between Korean and Japanese adolescents. On this basis, we proposed measures emphasizing the importance of health, to enhance Korean and Japanese adolescents’ performance. Conclusions: It is important for national government, public education institutions, and families to couple a therapeutic approach with a preventive and management approach that encourages periodic exercise, desirable diet, and adequate sleep when exploring measures to maintain and promote adolescents’ health.