<p>This study compared family functioning among families of children with anxiety disorders, with and without autism spectrum disorder (ASD), and typically developing children. We evaluated (1) group differences in family functioning, (2) changes in family functioning following child-focused cognitive behavioral therapy for anxiety, and (3) whether pre-treatment family functioning predicted anxiety reduction. Participants were 264 children (aged 7–18&#xa0;years) and their parents (251 mothers and 172 fathers). Groups consisted of children with anxiety disorders without ASD (<i>n</i> = 95), children with both conditions (<i>n</i> = 79), and typically developing children (<i>n</i> = 90). Children and parents completed the Family Functioning Scale, which assesses relational functioning and system maintenance. As expected, families of children with both anxiety disorders and ASD reported lower relational functioning and higher system maintenance than controls. System maintenance was also higher in these families than in the anxiety-only group (per both parents). Unexpectedly, the anxiety-only group did not differ from the control group. Additionally, cognitive behavioral therapy did not improve family functioning in either clinical group, nor did pre-treatment family functioning predict anxiety reductions. Families of children with both anxiety and ASD showed poorer family functioning than both other groups. Future research should examine whether these challenges stem from their co-occurrence or are specific to ASD.</p>