The prevalence of pain in children and adolescents with psychiatric conditions is rarely investigated. The aims of the current study were to (a) describe the prevalence of headaches and abdominal pain in children and adolescents with psychiatric conditions, (b) compare the prevalence of pain in children and adolescents with psychiatric conditions with that in the general population, and (c) investigate the associations between pain experience and different types of psychiatric diagnoses. Families with a child aged 6-15 years who had been referred to a child and adolescent psychiatry (CAP) clinic completed the Chronic Pain in Psychiatric Conditions questionnaire. Information about the child/adolescent's psychiatric diagnosis(es) was extracted from the CAP clinic's medical records. The children and adolescents included in the study were divided into diagnostic groups and compared. Their data were also compared with data of control subjects collected during a previous study of the general population. Abdominal pain was more common among girls with a psychiatric diagnosis (85%) than in the matched control population (62%, p = 0.031). Children and adolescents with neurodevelopmental diagnoses had a higher prevalence of abdominal pain than children and adolescents with other psychiatric diagnoses. Pain conditions in children and adolescents with a psychiatric diagnosis are common and must be addressed.