Little is known about the alliance between therapists and children with autism spectrum disorder who are receiving psychological therapies in outpatient treatment settings. This study examined the therapeutic alliance in children with autism spectrum disorder and clinical anxiety, who were receiving cognitive behavioral therapy in a randomized, controlled trial. The Therapeutic Alliance Scale for Children was administered to a sample of children and youth with autism spectrum disorder and anxiety (N = 64; aged 7-14) as well as to their parents and therapists. A comparison sample of typically developing youth with clinical anxiety (N = 36; aged 5-12) was included. The child-therapist alliance was more positive among typically developing children than among children with autism spectrum disorder; correspondingly, the parent-therapist alliance was also more positive among parents of typically developing children. Therapist reports of positive child-therapist alliance predicted post-treatment reductions in anxiety among children with autism spectrum disorder, although child reports of this alliance did not. Parent reports of positive parent-therapist alliance also predicted post-treatment reductions in the child's anxiety in the group with autism spectrum disorder. A strong therapeutic alliance appears to be associated with better treatment outcomes in children with autism spectrum disorder receiving cognitive behavioral therapy, although a thoughtful and diagnostically sensitive approach is advisable to promote a positive alliance with children with autism spectrum disorder.