Abstract Chronic pain is a common issue worldwide and remains a big challenge to physicians, particularly when the underlying causes do not meet any specific disease for settlement. Such medically unexplained somatic symptoms of pain that lack an integrated diagnosis in medicine have a high psychiatric comorbidity such as depression, and will require a multidisciplinary treatment strategy for a better outcome. Thus, most patients deserted management in spite of being inadequately treated and even presented with high resistance to analgesic drugs. Noninvasive brain stimulation, including repetitive transcranial magnetic stimulation (rTMS), has been used to treat refractory neuropathic pain and the analgesic efficacy is promising. So far, some case series and randomized rTMS studies have reported on patients with certain medically unexplained symptoms (MUSs) of pain (e.g., psychogenic pain or somatic symptoms in major depression and fibromyalgia). However, there is still no review article that is specific to the efficacy of rTMS on chronic unexplained symptoms of pain. Therefore, in the present review, we ventured to clarify the terminology and summarized the analgesic effects of rTMS on chronic MUSs of pain.