Background Obsessive-compulsive disorder (OCD) is a debilitating and prevalent anxiety disorder. Although the basal ganglia and frontal cortex are the brain regions that are most commonly hypothesized to be involved in OCD, the exact pathophysiology is unknown. By observing the effects of proven treatments on brain activation levels, the cause of OCD can be better understood. Currently, the gold standard treatment for OCD is cognitive behavioral therapy (CBT) with exposure and response prevention. However, this is often temporally and geographically inaccessible, time consuming, and costly. Fortunately, CBT can be effectively delivered using the internet (electronically delivered CBT [e-CBT]) because of its structured nature, thus addressing these barriers. Objective The aims of this study are to implement an e-CBT program for OCD and to observe its effects on brain activation levels using functional magnetic resonance imaging (MRI). It is hypothesized that brain activation levels in the basal ganglia and frontal cortex will decrease after treatment. Methods Individuals with OCD will be offered a 16-week e-CBT program with exposure and response prevention mirroring in-person CBT content and administered through a secure web-based platform. The efficacy of the treatment will be evaluated using clinically validated symptomology questionnaires at baseline, at week 8, and after treatment (week 16). Using functional MRI at baseline and after treatment, brain activation levels will be assessed in the resting state and while exposed to anxiety-inducing images (eg, dirty dishes if cleanliness is an obsession). The effects of treatment on brain activation levels and the correlation between symptom changes and activation levels will be analyzed. Results The study received initial ethics approval in December 2020, and participant recruitment began in January 2021. Participant recruitment has been conducted through social media advertisements, physical advertisements, and physician referrals. To date, 5 participants have been recruited. Data collection is expected to conclude by January 2022, and data analysis is expected to be completed by February 2022. Conclusions The findings from this study can further our understanding of the causation of OCD and help develop more effective treatments for this disorder. Trial Registration ClinicalTrials.gov NCT04630197; https://clinicaltrials.gov/ct2/show/NCT04630197. International Registered Report Identifier (IRRID) PRR1-10.2196/30726