This study aims to investigate the changes in the structural relationship between alienation in physical education (PE) class, school happiness, and future healthy life expectancy in Korean adolescents after the COVID-19 pandemic. The data were collected from adolescents in the Republic of Korea using scales for these factors. The collected data were analyzed with frequency analysis, reliability analysis, validity analysis, independent t-test, and path analysis. The key results were as follows. First, there were partial changes in each of the parameters since the outbreak of COVID-19. Second, before the pandemic, alienation in PE class negatively affected school happiness, and school happiness positively affected future healthy life expectancy; however, alienation in PE class did not affect future healthy life expectancy showing a complete mediating effect. Third, during the pandemic, alienation in PE class negatively affected school happiness, and school happiness positively affected future healthy life expectancy; alienation in PE class negatively affected future healthy life expectancy, showing a partial mediating effect. These findings emphasize the importance and potential of school education, especially PE, in promoting happiness and healthy life in adolescents. We expect these findings to have practical implications for future research by presenting theoretical and empirical data.