The aim is to estimate the prevalence and evaluate the association of socioeconomic and lifestyle factors with skipping breakfast among Brazilian adolescent students. A cross-sectional study carried out with adolescent ninth-graders from Brazilian public and private schools participating in the 2015 National School Health Survey. The prevalence of skipping breakfast (less than five days/week) and its respective 95% confidence intervals were estimated and stratified by gender according to demographic, socioeconomic, and lifestyle factors, self-perceived body image, and attitudes towards weight. A three-block hierarchical Poisson regression, considering the complex sample design. The prevalence of skipping breakfast was 35.6%, higher among girls than boys. In both genders, skipping breakfast was positively associated with the highest socioeconomic level, morning school shift, paid work, regular consumption of alcoholic beverages, living only with the mother, the father or neither, the irregular consumption of school food and meals with parents, considering oneself too fat/fat and trying to lose weight. In general, skipping breakfast was associated with socioeconomic factors and lifestyle behaviors harmful to health among adolescent students.