Emotional and behavioural problems occur more commonly in children with Autism Spectrum Disorder (ASD) compared to other children. Few studies have focused on these problems in children with ASD attending mainstream schools. We assessed via parent report the emotional and behavioural problems in 160 children aged 4-17 years with ASD attending mainstream schools and investigated differences between the primary and secondary aged children. Children with ASD had higher levels of problems across all domains of the Strengths and Difficulties Questionnaire (SDQ) compared to UK norms. Within the ASD sample, SDQ scores were associated with male sex, living in a household with more children, more severe autism symptoms and fewer adaptive skills, and higher levels of family socio-economic risk. No robust primary-secondary school differences were found. Implications for future research and the support of children with ASD in mainstream school settings are discussed.