Children with autism spectrum disorder (ASD) experience obsessions and compulsions similar to those specified in DSM-5 for obsessive compulsive disorder yet little controlled research exists on treating these behaviours. Thirty-seven children (7-13 years old) were randomly assigned to a 9-week functional behavior-based cognitive behavior therapy (Fb-CBT) or Treatment As Usual. Independent assessors administered measures pre- and post-treatment and at 6-months. Two primary outcome measures indicated statistically significant differences between groups, with large corrected effect sizes (Hedge's g = 1.00 and 1.15, respectively). This is the first known RCT to exclusively treat obsessive compulsive behaviors (OCBs) in children and youth with high functioning (IQ ≥ 70) ASD, and suggests that Fb-CBT treatment shows promise in decreasing these behaviors and improving quality of life. Trial Registration This trial was registered with ClinicalTrials.gov (ID: NCT03123146).