Background: Although disparities in socioeconomic status in health behaviors have been highlighted globally, they are not well understood in Japanese adolescents. The purpose of this study was to clarify the changes in socioeconomic disparities in adolescents’ fundamental health behaviors, such as physical activity, screen time (ST), sleep, breakfast intake, and bowel movement before and during COVID-19. Methods: This was a repeated cross-sectional study which used data from the 2019 and 2021 National Sports-Life Survey of Children and Young in Japan. Data of 766 and 725 participants in 2019 and 2021, respectively, were analyzed. Favorable health behaviors were defined as daily moderate to vigorous physical activity (MVPA) of at least 60 minutes, ST of less than 2 hours, sleep of 8 to 10 hours, daily breakfast intake, and bowel movement frequency of at least once in every 3 days. We calculated the slope index of inequality and relative index of inequality in each health behavior for equivalent household income levels for assessing absolute and relative economic inequalities. Results: Compliance with MVPA and ST recommendation significantly declined from 20.1% and 23.0% in 2019 to 11.7% and 14.9% in 2021, respectively. The slope index of inequality and relative index of inequality increased in MVPA for income levels, but decreased in daily breakfast in 2019 to 2021. Although the widening and narrowing of the disparity were inconclusive for ST, it exacerbated for the higher-income groups. Conclusions: Our study revealed widening of economic disparities in the achievement of recommended MVPA and narrowing of it in breakfast intake among adolescents before and during COVID-19.