Children with neurodevelopmental disorders often have social-emotional and behavioural difficulties. The present study explored these difficulties in children (n = 50, aged 6–10 years) with autism spectrum disorder, attention-deficit/hyperactivity disorder and developmental language disorder. Parents, teachers and therapists evaluated children’s social-emotional and behavioural difficulties through a self-devised questionnaire and the Strengths and Difficulties Questionnaire. Additionally, the children, along with their typically developing age peers (n = 106), completed six emotion discrimination tasks. Analysis revealed some impaired emotion discrimination skills that were predictive for behavioural challenges in daily life and associated with the parent-reported existence of friends. Timely intervention in these children is needed, and it should also include emotion perception training.