Background <p>School racial segregation, a key manifestation of structural racism, has been hypothesized to cause poorer health among Black individuals, contributing to racial health inequities across the life course. School segregation has been increasing in the past 30&#xa0;years in the US. Few studies have examined the association between school racial segregation and children’s health.</p> Methods <p>We linked school district-level segregation measures to individual-level panel data from the 1997–2001 waves of the National Longitudinal Study of Youth 1997. We included Black and White in-school children who reported self-rated health, body weight, and alcohol- and smoking-related behaviors. We fitted standard ordinary least squares (OLS) models (capturing between-person variation), then individual-level fixed effect (FE) models (capturing within-person variation) to reduce bias from any unmeasured confounding. All models were adjusted for individual-, neighborhood-, and district-level covariates.</p> Results <p>Results from OLS models suggest that school segregation was associated with a later age of smoking initiation among Black youths (0.46; 95% CI 0.22, 0.71). Results from FE models suggest that school segregation was associated with worse self-reported health (− 3.9% points; 95% CI − 7.4, − 0.42) and a higher probability of ever smoking (3.2% points; 95% CI 0.67, 5.7) among Black youths. School segregation was not associated with White youths’ health outcomes.</p> Conclusions <p>Increases in US school segregation may shape Black youths’ health behaviors and well-being, laying the groundwork for poorer adult health. Policies to reduce school segregation may be beneficial for Black children’s health and may reduce health inequities.</p>