Background: Few studies have examined the link between child-therapist alliance and outcome in manual-guided cognitive behavioral therapy (CBT) for children diagnosed with anxiety disorders. This study sought to clarify the nature and strength of this relation. Methods: The Therapy Process Observational Coding System for Child Psychotherapy-Alliance scale (TPOCS-A; McLeod, 2005) was used to assess the quality of the child-therapist alliance. Coders independently rated 123 CBT therapy sessions conducted with 34 children (aged 6-13 years) diagnosed with anxiety disorders. Parents reported on children's symptomatology at pre- mid-, and post-treatment. Results: A stronger child-therapist alliance early in treatment predicted greater improvement in parent-reported outcomes at mid-treatment but not post-treatment. However, improvement in the child-therapist alliance over the course of treatment predicted better post-treatment outcomes. Conclusions: The quality of the child-therapist alliance assessed early in treatment may be differentially associated with symptom reduction at mid- and post-treatment. Results underscore the importance of assessing the relation between alliance and outcome over the course of therapy to clarify the role the child-therapist alliance plays in child psychotherapy.