Background The impact of behavioral disorders on custodial school-engagement has not been studied. We investigated the impact of conduct disorder (CD), oppositional-defiant disorder (ODD), and attention deficit/ hyperactivity disorder (ADHD) on the level of school-engagement among detained boys in a youth correctional facility in Lagos, Nigeria. Methods A total of 103 boys were assessed, at the point of remand, for the presence or otherwise of behavioral disorders using the DSM-5 version of the Kiddie Schedule for Affective Disorders and Schizophrenia. The level of emotional, behavioral, and cognitive school-engagement among them was also assessed, using the School Engagement Measure, three months after enrolment in the custodial school. Results More than half of respondents had at-least one behavioral disorder, with CD being the most prevalent (54.4%). Multiple regression analyses showed that after controlling for perceived autonomy of learning climate, age, and prior level of education at baseline; each of the three behavioral disorders assessed had an independent negative impact on self-reported level of school-engagement three months after enrolment in custodial school. Among the behavioral disorders, ADHD had the largest magnitude of impact (β=-2.78; p<0.01). Conclusions We concluded that behavioural disorders had negative impact on school engagement in youth correctional settings and constitute potential barrier to successful educational rehabilitation.