The literature emphasizes that the school environment is a key factor for the mental health and academic achievement of immigrant and refugee children. However, few studies examined the role of school environment and peer relationships for these youth attending a special education class. The aim of this paper is to study the association between emotional difficulties and academic performance and their correlates in first and second generation immigrants assigned to a special class in a multiethnic environment. The results emphasize the need to adopt an eco-systemic model to understand the complex and probably bidirectional relations between the mental health symptoms and academic performance in immigrant adolescents identified as having difficulties by the school system. The salience of peer relations and classroom environment suggests that schools need to promote positive school-based relationships to improve immigrant adolescent mental health.