Background: Exclusionary discipline (ED) has long been an educational equity concern, but its relationship with student health and protective factors is less understood. Methods: Using population-based public school student data (N = 82,216), we examined associations between past-month ED and positive depression and anxiety screening instrument results. We also assessed whether each of 9 potential protective factors moderated the ED-mental health relationship by testing interaction effects. Results: Over 1 in 10 youth experienced past-month ED, with variation by sex, gender identity, special education status, poverty, region, race/ethnicity, and adverse childhood experiences. Net of sociodemographic factors, youth who experienced ED had higher likelihood for current depression (adjusted odds ratio [AOR]: 1.64, 95% confidence interval [CI]: 1.55, 1.73) and anxiety (AOR: 1.49, 95% CI: 1.41, 1.58) symptoms. Significant associations were robust across 5 racial/ethnic groups, except for anxiety among American Indian/Alaska Native youth. Individual, interpersonal, and school-level protective factors appeared to mitigate depression and anxiety regardless of disciplinary experience. Implications for School Health Policy, Practice, and Equity: Our findings document ED disproportionality and possible ramifications for emotional well-being. Conclusions: In concert with structural efforts to reduce reliance on ED, strategies that bolster protective factors may support youth already impacted by ED and/or mental health problems.