Recent studies reported that the age of primary school enrolment is a major driver of educational achievement and adult income, but its impacts on childhood health and nutrition remain largely unknown, particularly in developing countries where childhood stunting and overweight coexist. In Brazil, children are supposed to enrol in primary school the year they turn 6. Using a database of middle school students in Brazil based on a 2015 survey, I implemented an instrumental variables strategy using quasi-exogenous variations in the students' birthdates to isolate the impact of late primary school enrolment (i.e., older than 6 when enrolled) on height-forage and body mass-forage indicators. Overall, late enrolment has protective effects against hazardous weight gain (− 0.14 z-score unit) but significantly increases the risk of moderate stunting (by 1.5% points). Heterogeneity in family backgrounds may explain these results. Indeed, delayed school enrolment is particularly detrimental for the nutritional status of students from underprivileged settings. In terms of public policy, rather than changing school starting age, this study highlights the importance of focusing on pathways to fight both stunting and overweight conditions in Brazilian children.