Treatment-resistant depression (TRD) is the inability of a patient with major depressive disorder (MDD) to accomplish or achieve remission after an adequate trial of antidepressant treatments. Several combinations and augmentation treatment strategies for TRD exist, including the use of repetitive transcranial magnetic stimulation (rTMS), and new therapeutic options are being introduced. Text4Support, a text message-based form of cognitive behavioral therapy that allows patients with MDD to receive daily supportive text messages for correcting or altering negative thought patterns through positive reinforcement, may be a useful augmentation treatment strategy for patients with TRD. It is however currently unknown if adding the Text4Support intervention will enhance the response of patients with TRD to rTMS treatment. This study aims to assess the initial comparative clinical effectiveness of rTMS with and without the Text4Support program as an innovative patient-centered intervention for the management of patients diagnosed with TRD. This study is a multicenter, prospective, parallel-design, 2-arm, rater-blinded randomized controlled pilot trial. The recruitment process is scheduled to last 12 months. It will involve active treatment for 6 weeks, observation, and a follow-up period of 6 months for participants in the study arms. In total, 200 participants diagnosed with TRD at rTMS care clinics in Edmonton, Alberta, and rTMS clinics in Halifax, Nova Scotia will be randomized to 1 of 2 treatment arms (rTMS sessions alone or rTMS sessions plus Text4Support intervention). Participants in each group will be made to complete evaluation measures at baseline, and 1, 3, and 6 months. The primary outcome measure will be the mean change in the scores of the Patient Health Questionnaire-9 (PHQ-9). The secondary outcome measures will involve the scores of the 7-item Generalized Anxiety Disorders Scale (GAD-7), Columbia-Suicide Severity Rating Scale (CSSRS), and World Health Organization-Five Well-Being Index (WHO-5). Patient data will be analyzed with descriptive statistics, repeated measures, and correlational analyses. Qualitative data will be analyzed using the thematic analysis framework. The results of the study are expected to be available 18 months from the start of recruitment. We hypothesize that participants enrolled in the rTMS plus Text4Support intervention treatment arm of the study will achieve superior outcomes compared with the outcomes of participants enrolled in the rTMS alone arm. The application of the combination of rTMS and Text4Support has not been investigated previously. Therefore, we hope that this study will provide a concrete base of data to evaluate the practical application and efficacy of using the novel combination of these 2 treatment modalities. PRR1-10.2196/46830.