The aim of this study was to analyze the association between adherence to school meals and the co-occurrence of the regular consumption of healthy and unhealthy eating markers among Brazilian adolescents. Data from 67,881 adolescents in Brazilian public schools who participated in the 2015 National School Health Survey, were used. From the 7-day FFQ, the dependent variable was constructed, co-occurrence of regular consumption (≥ 5x/week) of healthy and unhealthy food markers, which was categorized as regular consumption of none, one or two, or three eating markers. We performed an ordinal logistic regression with adjustment for sociodemographic, eating habits outside of school, and school characteristics variables. The prevalence of the co-occurrence of the regular consumption of three healthy eating markers was 14.5%, and that of three unhealthy markers was 4.9%. High adherence to school meals (every day) was positively associated with regular consumption of healthy eating markers and inversely associated with regular consumption of unhealthy eating markers. The school meals provided by PNAE contribute to the promotion of healthy eating habits among Brazilian adolescents.