Therapeutic alliance is often an important aspect of psychotherapy, though it is rarely examined in clients with autism. This study aims to determine the child pre-treatment variables and treatment outcomes associated with early and late alliance in cognitive behaviour therapy targeting emotion regulation for children with autism. Data were collected from 48 children with autism who participated in a larger randomized-controlled trial. Pre-treatment child characteristics included child, parent, and clinician report of child emotional and behavioural functioning. Primary outcome measures included child and parent-reported emotion regulation. Therapeutic alliance (bond and task-collaboration) was measured using observational coding of early and late therapy sessions. Pre-treatment levels of child-reported emotion inhibition were associated with subsequent early and late bond. Pre-treatment levels of parent and child-reported emotion regulation were related to early and late task-collaboration. Late task-collaboration was also associated with pre-treatment levels of behavioural and emotional symptom severity. Task-collaboration in later sessions predicted improvements in parent-reported emotion regulation from pre- to post-therapy. Future research is needed to further examine the role of task-collaboration as a mechanism of treatment change in therapies for children with autism.