Most studies of the relationship between racial segregation and racial health disparities have focused on residential segregation. School-based racial segregation is an additional form of segregation that may be associated with racial disparities in health. This study examines the relationship between both residential segregation and school segregation and racial health disparities among non-Hispanic Black compared to non-Hispanic White persons at the county level in the United States. It also examines the relationship between changes in residential and school segregation and subsequent trajectories in a variety of racial health disparities across the life course. Using the CDC WONDER Multiple Case of Death database, we derived an annual estimate of race-specific death rates and rate ratios for each county during the period 2000-2020. We then examined the relationship between baseline levels of residential and school segregation in 1991 as well as changes between 1991-2000 and the trajectories of the observed racial health disparities between 2000 and 2020. We used latent trajectory analysis to identify counties with similar patterns of residential and school segregation over time and to identify counties with similar trajectories in each racial health disparity. Outcomes included life expectancy, early mortality (prior to age 65), infant mortality, firearm homicide, total homicide, and teenage pregnancy rates. During the period 1991-2020, racial residential segregation remained essentially unchanged among the 1051 counties in our sample; however, racial school segregation increased during this period. Increases in school segregation from 1991 to 2000 were associated with higher racial disparities in each of the health outcomes during the period 2000-2020 and with less progress in reducing these disparities. This paper provides new evidence that school segregation is an independent predictor of racial health disparities and that reducing school segregation-even in the face of high residential segregation-could have a long-term impact on reducing racial health disparities. Furthermore, it suggests that the health consequences of residential segregation have not been eliminated from our society but are now being exacerbated by a new factor: school-based segregation. Throughout this paper, changes in school-based segregation not only show up as a consistent significant predictor of greater racial disparities throughout the life course, but at times, an even stronger predictor of health inequity than residential segregation.