Neuropathic pain, affecting 6.9–10% of the general population, has a negative impact on patients’ quality of life and potentially leads to functional impairment and disability. Repetitive transcranial magnetic stimulation (rTMS)—a safe, indirect and non-invasive technique—has been increasingly applied for treating neuropathic pain. The mechanism underlying rTMS is not yet well understood, and the analgesic effects of rTMS have been inconsistent with respect to different settings/parameters, causing insufficient evidence to determine its efficacy in patients with neuropathic pain. This narrative review aimed to provide an up-to-date overview of rTMS for treating neuropathic pain as well as to summarize the treatment protocols and related adverse effects from existing clinical trials. Current evidence supports the use of 10 Hz HF-rTMS of the primary motor cortex to reduce neuropathic pain, especially in patients with spinal cord injury, diabetic neuropathy and post-herpetic neuralgia. However, the lack of standardized protocols impedes the universal use of rTMS for neuropathic pain. rTMS was hypothesized to achieve analgesic effects by upregulating the pain threshold, inhibiting pain impulse, modulating the brain cortex, altering imbalanced functional connectivity, regulating neurotrophin and increasing endogenous opioid and anti-inflammatory cytokines. Further studies are warranted to explore the differences in the parameters/settings of rTMS for treating neuropathic pain due to different disease types.