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Background: To mitigate the negative impacts of the pandemic, it is essential to understand how the associations between different types of physical activity (PA) and adolescent well-being changed before and after the COVID-19 pandemic (defined here as the period marked by students’ return to stable in-person education). This study aimed to examine gender differences in the associations between school-related PA and subjective well-being before and after the pandemic. Methods: A cross-sectional design was used, including 430 boys and 571 girls from 22 high schools. Participants completed the Youth Activity Profile questionnaire to assess school-related and school-associated PA and the WHO-5 Well-Being Index to evaluate subjective well-being. Differences in participants’ PA across segments of the school day before and after the pandemic were evaluated using the Kruskal–Wallis test, and compliance with PA recommendations was analyzed using cross-tabulation and Pearson’s chi-square tests. Results: After the pandemic, both boys and girls reported significantly lower levels of active transportation to and from school compared with the pre-pandemic period. In addition, well-being levels were significantly lower in both genders after the pandemic. Before the pandemic, boys and girls with higher well-being met the recommendations for PA to school, from school, and outside of school significantly more often than their peers with lower well-being. Higher levels of well-being were observed both before and after the pandemic in boys and girls who participated in organized PA compared with non-participants. Conclusions: This study confirms lower levels of PA and well-being among adolescents after the pandemic. In particular, PA to and from school was at a lower level after the pandemic than before the pandemic. Participation in organized PA was significantly associated with higher well-being in both boys and girls before and after the pandemic. Supporting adolescents’ participation in organized PA should be a priority when addressing the negative consequences of societal crisis situations. Improved knowledge of the associations between PA and well-being may contribute to more effective support for adolescents’ PA and greater awareness of the importance of meeting PA recommendations.