INTRODUCTION: While multiple pharmacological and non-pharmacological interventions treating chronic non-specific low back pain (CLBP) are available, they have been shown to produce at best modest effects. Interventions such as repetitive transcranial magnetic stimulation (rTMS), a form of non-invasive brain stimulation, have exhibited promising results to alleviate chronic pain. However, evidence on the effectiveness of rTMS for CLBP is scarce due to limited rigorous clinical trials. Combining rTMS with motor control exercises (MCE) may help to address both central and nociceptive factors contributing to the persistence of LBP. The primary aim of this randomised controlled trial is to compare the effectiveness of a combination of rTMS and MCE to repeated rTMS sessions alone, sham rTMS and a combination of sham rTMS and MCE on pain intensity. METHODS AND ANALYSIS: One hundred and forty participants (35/group) with CLBP will be randomised into four groups (active rTMS+MCE, sham rTMS+MCE, active rTMS and sham rTMS) to receive 10 sessions of their allocated intervention. The primary outcome will be the pain intensity, assessed at baseline, 4, 8, 12 and 24 weeks. Secondary outcomes will include disability, fear of movement, quality of life and patient global rating of change. ETHICS AND DISSEMINATION: Ethics approval was obtained from the in June 2019 (#2020-1844 - CER CIUSSS-CN). The results of the study will be submitted to a peer-reviewed journal and scientific meetings. TRIAL REGISTRATION NUMBER: NCT04555278.