Black men and women have different levels of average educational attainment, yet few studies have focused on explaining how and why these patterns develop. One explanation may be inequality in experiences with institutional punishment through exclusionary school discipline and criminal justice exposure. Drawing on intersectional frameworks and theories of social control, I examine the long-term association between punishment and the Black gender gap using data from the Children of the National Longitudinal Survey of Youth 1979 cohort (NLSY-C). Decomposition analyses reveal that about one third of the gender gap can be explained by gender differences in experiences with institutional punishments, net of differences in observed behaviors. These measures are predictive at key educational transition points, including finishing high school and earning a 4-year college degree. Though Black boys and girls have similar family backgrounds and grow up in similar neighborhoods, results suggest that Black girls have a persistent advantage in educational attainment due in part to their lower levels of exposure to exclusionary school discipline and the criminal justice system. In addition, I find that gender differences in early achievement, early externalizing behavioral problems, school experiences, and substance use in adolescence and early adulthood are associated with gender differences in educational attainment. Taken together, these results illustrate the importance of punishment disparities in understanding disparate educational outcomes over the life course of Black men and women.