We compared the effects of a 16-week Cognitive-Behavioral Therapy (CBT) program and a Social Recreational (SR) program on anxiety in children with Autism Spectrum Disorders (ASD). Seventy children (9–16 years old) were randomly assigned to either of the programs (n CBT = 36; n SR = 34). Measures on child’s anxiety using the Spence Child Anxiety Scale—Child (SCAS-C) and the Clinical Global Impression—Severity scale (CGI-S) were administered at pre-, post-treatment, and follow-ups (3- and 6-month). Children in both programs showed significantly lower levels of generalized anxiety and total anxiety symptoms at 6-month follow-up on SCAS-C. Clinician ratings on the CGI-S demonstrated an increase in the percentage of participants rated as “Normal” and “Borderline” for both programs. Findings from the present study suggest factors such as regular sessions in a structured setting, consistent therapists, social exposure and the use of autism-friendly strategies are important components of an effective framework in the management of anxiety in children and adolescents with ASD.