Cognitive Behavioural Therapy (CBT) programs adapted to children with Autism Spectrum Disorder (ASD) effectively reduce anxiety when run in university clinics. Forty-nine children aged 8–14 years participated in a waitlist controlled study in a general child psychiatric hospital setting. Post-treatment 30% of the children were free of their primary anxiety diagnoses and 5% were free of all anxiety diagnoses. No statistically significant difference between the two trial conditions were found on primary outcomes. However, statistically significant differences were found on secondary outcomes indicating clinically meaningful treatment responses. Together with high program satisfaction this study shows the CBT program to be feasible and potentially efficacious in treating anxiety in children with ASD in a general child psychiatric hospital setting.