Background: Obsessive-Compulsive Disorder (OCD) is a common chronic psychiatric disorder that constitutes a leading cause of disability. Although Cognitive-Behaviour Therapy (CBT) has been shown to be an effective treatment for OCD, this specialised treatment is unavailable to many due to access issues and the social stigma associated with seeing a mental health specialist. Internet-based psychological treatments have shown to provide effective, accessible and affordable treatment for a range of anxiety disorders, and two Randomised Controlled Trials (RCTs) have demonstrated the efficacy and acceptability of internet-based CBT (iCBT) for OCD, as compared to waitlist or supportive therapy. Although these initial findings are promising, they do not isolate the specific effect of iCBT. This paper details the study protocol for the first randomised control trial evaluating the efficacy of therapist-assisted iCBT for OCD, as compared to a matched control intervention; internet-based therapist-assisted progressive relaxation training (iPRT). It will aim to examine whether therapist-assisted iCBT is an acceptable and efficacious treatment, and to examine how effectiveness is influenced by patient characteristics. Method/design: A randomised controlled trial using repeated measures with two arms (intervention and matched control) will be used to evaluate the efficacy and acceptability of iCBT for OCD. The RCT will randomise 212 Australian adults with a primary diagnosis of OCD into either the active intervention or control condition, for 12 weeks duration. Outcomes for participants in both study arms will be assessed at baseline and post-intervention. Participants in iCBT will be further assessed at six month follow-up, while participants in the control condition will be crossed over to receive the iCBT intervention and reassessed at post-intervention and six month follow-up. The primary outcome will be clinically significant change in obsessive-compulsive symptom scores. Discussion: This will be the first known therapist assisted internet-based trial of a comprehensive CBT treatment for OCD as compared to a matched control intervention. Demonstrating the efficacy of an internet-based treatment for OCD will allow the development of models of care for broad-based access to an evidence-based but complex treatment.