Objective The health behavior and mental health problems of adolescents have shown a variety of changes due to the coronavirus disease-2019 (COVID-19) pandemic. This study compared health behavior, obesity, and mental health among Korean adolescents before and during the early COVID-19 pandemic. Methods Population-based and cross-sectional data from the 2019 and 2020 Korea Youth Risk Behavior Web-Based Surveys were used. Data of 57,048 and 54,948 adolescents from the 2019 and 2020 surveys, respectively, were compared. Multiple logistic regression analysis was conducted to compare health behavior, obesity, and mental health before and during the COVID-19 pandemic. Results The adjusted odds ratio (aOR) of overweight, obesity, and body image perceived subjectively as fat, were higher in the 2020 sample compared to the 2019 sample. The aOR of the frequency (more than 3 times a week) of fast-food consumption was higher in 2020 than in 2019. However, the aOR of physical activity, alcohol use, and smoking experience were lower in 2020 than in 2019. In addition, during COVID-19, adolescents were less likely to have perceived severe stress, depressive moods, and suicidal ideation. Conclusion Current evidence suggests the co-occurrence of positive and negative changes in health behavior, obesity, and mental health among Korean adolescents during the early COVID-19 pandemic. The results contribute insights for monitoring adolescents’ health behavior and promoting their mental health during school shutdowns.