Concern is growing over the limited academic progress in special education students with emotional and/or behavioral disorders (EBD). We know little about how academic and behavioral factors interact in these students to affect their academic functioning. Therefore, potential associations were investigated over the course of one school year for 196 secondary students with EBD in a self-contained public school (SCS). Demographics, IQ and achievement testing, teacher checklist ratings for emotional/ behavioral problems, and standard measures of school function were gathered. First, academic achievement was studied, and regression analyses showed that both reading and math achievement were significantly increased by higher verbal IQ and lower ADHD-inattentive symptoms (ADHD-I), and math also by higher performance IQ and younger age. Next, general academic performance was examined, and regression analysis demonstrated that major-subject GPA was significantly increased by lower ADHD-I teacher ratings, higher math achievement, and younger age. In comparison, out-of-school suspensions were significantly increased by higher conduct disorder and lower social phobia ratings. Thus, in these students with EBD in an SCS, academic functioning was primarily affected by academic parameters, and by ADHD-I but not by other emotional/behavioral problems. These results can further inform the planning of academic interventions for many students with EBD.