Teachers play a key role in creating effective conditions for students to succeed in school. The quality of student–teacher relationships is consistently associated with social, emotional, behavioural and academic adjustment, and this is even more relevant for students with special educational needs (SEN), considering these students’ emotional, social and learning vulnerabilities. This study aimed to examine the associations between students’ externalising and internalising behaviour, social skills and academic performance, and teachers’ perceptions of conflict and closeness in their relationships with students with and without SEN. Data regarding 360 students in Year 3, Year 5 and Year 7 (169 students with SEN) were collected. Teachers (n = 74) reported on the student–teacher relationship and students’ social skills, behaviour problems and academic performance. Special education teachers (n = 38) provided information regarding the diagnosis and profile of functioning of students with SEN. Results showed that teachers’ reports of students’ social skills and externalising problems were the strongest predictors of closeness and conflict. Internalising problems and SEN status also predicted decreased closeness, despite smaller effects. Taken together, findings support the importance of professional development opportunities focusing on facilitating teachers’ relationships with students with perceived challenging behaviour.