Purpose: This study aimed to investigate the association between sedentary behavior and generalized anxiety disorder (GAD) according to changes in physical activity after coronavirus disease 2019 (COVID-19) in Korean adolescents. Methods: This study included 52,723 South Korean middle and high school students who had obtained a complete Korea youth risk behavior survey, 2021. To identify the association between sitting time and GAD (GAD-7 scale≥10), odds ratio (OR) and 95% confidence interval (CI) were calculated using complex sample logistic regression analysis (p＜0.05). Results: After adjusting for confounding variables, higher sitting time was associated with higher GAD risk (OR [95% CI]: 5–10 hours, 1.15 [1.04–1.27]; 10–15 hours, 1.23 [1.12–1.35]; ≥15 hours, 1.28 [1.15–1.43]). In adolescents whose physical activity has not changed or has increased after COVID-19, as the sitting time increased, the OR (95% CI) of GAD increased (5–10 hours, 1.15 [1.02–1.31]; 10–15 hours, 1.20 [1.07–1.35]; ≥15 hours, 1.35 [1.17–1.54]). But, not in adolescents whose physical activity has decreased after COVID-19. Conclusion We observed the independent associations between sedentary behavior and GAD, and sedentary behavior and GAD are associated by change in physical activity after COVID-19 among adolescents. Therefore, in the pandemic era reducing sedentary behavior and increasing physical activity is necessary for adolescents to enhance mental health and decrease the case of GAD.