Objective: This article explores the relationship between childhood obesity and educational outcomes in Mexico, a country where excess weight is predominant. Design: Using complementary multivariate estimators, we empirically investigate the association between childhood excess weight, measured in 2002, and schooling attainment measured 10 years later. Non-linear specifications are tested, and heterogeneous effects according to gender, living area and economic backgrounds are investigated. Setting: To fill the literature gap, this study focuses on the understudied context of emerging countries such as Mexico. Participants: Panel data from the Mexican Family Life Survey (2002–2012) are used. We restricted the sample to adolescent individuals who had between 9 and 15 years old in 2002 (attended primary or secondary school in 2002). The survey provides an accurate follow-up information on weight, height and waist circumference for each individual. Results: Controlling for a comprehensive set of covariates, we find that the relationship is non-linear in Mexico. While weight-based childhood obesity and abdominal adiposity are significantly associated with lower school attainment, at least in urban settings, no schooling gap is found between overweight students and their normal-weight counterparts. Along with rural–urban heterogeneity, obesity-based educational penalties appear to be stronger for girls and students from privileged economic backgrounds. Conclusions: These results emphasise the co-occurrence of anti-fat and pro-fat social norms in Mexican schools: while anti-fat norms may particularly concern female, richer and urban students, pro-fat norms might persist among male, poorer and rural students. These findings have important implications for public policy, namely about awareness anti-obesity programmes.