Students with emotional and behavioral disorders (EBD) characteristically experience academic difficulties. There is growing evidence that the continuum from academic competence to underachievement is partially explained by executive function (EF; neurocognitive attention-regulation processes) and stress. Yet, there is scarce research investigating these relationships among students with or at risk for EBD, especially during the elevated stress and risk period of middle school, and particularly among racially/ethnically under-represented groups. Therefore, with 118 U.S. middle schoolers with or at risk for EBD and typical peers (70% Hispanic/Latinx; 25% Black), we examined group differences and relationships among perceived family, peer, and school stress, EF, and academic outcomes. When compared with their typical peers, students with or at risk for EBD scored lower on EF and academic tasks. For all students, higher EF predicted better academic functioning. Perceived stress was directly and negatively related with EF and indirectly associated with academic outcomes via EF.