In mainstream education, positive relationships with teachers and peers have been found to positively influence children’s behavioral development. However, high levels of classroom behavior problems may hinder the formation of such positive relationships. Therefore, findings from mainstream education cannot be generalized to special education. The present study investigated the developmental links between disobedience and positive as well as negative relationships with teachers and peers among boys in restrictive special educational settings. At three assessment waves across one school year, teacher-reports of teacher-child closeness and conflict, and peer-reports of peer acceptance, rejection and disobedience were collected among 340 boys (mean age = 10.1 years, SD = 1.58, range = 5–13) with psychiatric disorders receiving special education. Autoregressive cross-lagged models were fitted to explore the nature of these developmental links. The impact of boys’ age was examined using multiple group analyses. Findings supported the importance of teacher-child conflict, but not closeness, and positive and negative peer relationships for the development of boys’ disobedience, with a stronger effect of negative than positive relationships. However, teacher-child and peer relationships were not longitudinally related and the effect of boys’ age was minimal. This study extends prior research by suggesting that, despite differences in educational setting and severity of behavior problems between children in mainstream and special education, reducing negative classroom interactional patterns is most important in preventing the development of problematic classroom behavior in boys with severe social-emotional and behavioral difficulties.