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.