Obesity in adolescents is a global health concern associated with several diseases and complications in adulthood. Obesity has been reported to be strongly associated with oral habits. To investigate the association between tooth brushing during lunchtime and the prevalence of obesity among adolescents in a nationally representative sample of South Korean adolescents. Data from the 2018-2021 Korea Youth Risk Behavior Web-Based Survey were used in this cross-sectional study. Obesity was measured based on the body mass index. The chi-square test was used to investigate and compare tooth brushing habits during lunchtime in the study population, and multivariate logistic regression analysis was performed to analyze the relationship between tooth brushing during lunchtime and the prevalence of obesity. The odds of obesity were lower in the group that brushed their teeth during lunchtime (adjusted odd ratio: 0.90, 95% confidence interval: 0.88-0.93). Furthermore, the odds of obesity were significantly higher in high school students; boys; those with a low household income, low subjective health status awareness, medical history (asthma or atrophy), and history of sealant use; and those who responded after the coronavirus disease 2019 pandemic. A significant inverse relationship was found between tooth brushing habits during lunchtime and the prevalence of obesity. This relationship was consistent regardless of socioeconomic and lifestyle factors.