Despite the growing population of youth identifying with a transgender or nonbinary gender identity, research on gender diverse individuals’ educational outcomes is limited. This study takes advantage of the first nationally representative, population-based data set that includes measures of gender identity and educational outcomes: the High School Longitudinal Study of 2009. Using minority stress and structural symbolic interactionist frameworks, we examine the association between gender identity and high school and college educational outcomes. We compare educational outcomes of gender diverse youth—binary transgender, nonbinary, and gender unsure—to cisgender youth, and also examine differences within the gender diverse population. Given the strong link between minority stress and educational experiences among gender diverse youth, we examine differences in outcomes before and after accounting for school belonging and emotional distress. We also account for individuals’ social structural location, arguing that social positionality shapes both gender identity and educational outcomes. Results indicate important differences in educational outcomes within the gender diverse population: while binary transgender and gender unsure youth exhibit educational disadvantage, relative to cisgender youth, nonbinary youth do not. The gender unsure disadvantage remains even after accounting for differences in social structural location and social psychological factors associated with minority stress.