Background Major depression is a severe, disabling, and potentially lethal clinical disorder. Only about half of patients respond to an initial course of antidepressant pharmacotherapy. At least 15% of all patients with major depressive disorder (MDD) remain refractory to any treatment intervention. By the time that a patient has experienced 3 definitive treatment failures, the likelihood of achieving remission with the fourth treatment option offered is below 10%. Repetitive transcranial magnetic stimulation (rTMS) is considered a treatment option for patients with MDD who are refractory to antidepressant treatment. It is not currently known if the addition of internet-delivered cognitive-behavioral therapy (iCBT) enhances patients’ responses to rTMS treatments. Objective This study will evaluate the initial comparative clinical effectiveness of rTMS with and without iCBT as an innovative patient-centered intervention for the treatment of participants diagnosed with treatment-resistant depression (TRD). Methods This study is a prospective, two-arm randomized controlled trial. In total, 100 participants diagnosed with resistant depression at a psychiatric care clinic in Edmonton, Alberta, Canada, will be randomized to one of two conditions: (1) enrolment in rTMS sessions alone and (2) enrolment in the rTMS sessions plus iCBT. Participants in each group will complete evaluation measures (eg, recovery, general symptomatology, and functional outcomes) at baseline, 1 month, 3 months, and 6 months. The primary outcome measure will be the mean change to scores on the Hamilton Depression Rating Scale. Patient service utilization data and clinician-rated measures will also be used to gauge patient progress. Patient data will be analyzed with descriptive statistics, repeated measures, and correlational analyses. Results We expect the results of the study to be available in 24 months. We hypothesize that participants enrolled in the study who receive rTMS plus iCBT will achieve superior outcomes in comparison to participants who receive rTMS alone. Conclusions The concomitant application of psychotherapy with rTMS has not been investigated previously. We hope that this project will provide us with a concrete base of data to evaluate the practical application and efficacy of using a novel combination of these two treatment modalities (rTMS plus iCBT). Trial Registration ClinicalTrials.gov NCT0423965; https://clinicaltrials.gov/ct2/show/NCT04239651 International Registered Report Identifier (IRRID) PRR1-10.2196/18843