Background: Current clinical trials indicate that repetitive transcranial magnetic stimulation (rTMS) is effective in reducing drug‐resistant neuropathic pain (NP). However, there is a lack of studies evaluating the long‐term feasibility and clinical efficacy of rTMS in large patient cohorts in real‐world conditions. Methods: In this retrospective cohort study, we analysed 12 years of clinical data to assess the long‐term analgesic effects of 20 Hz rTMS over the primary motor cortex in patients with NP. Subgroup analyses were conducted to identify predictive factors and assess the potential role of epidural motor cortex stimulation (eMCS) as a sustained solution. Results In total, 193 patients completed test period of 4 rTMS sessions and 42% of them reported a pain relief (PR) greater than 30%, with concurrent improvement in their most disabling symptom. Iterative rTMS sessions maintained analgesic effects over 10 years in certain patients identified as responders (≥10% PR) without adverse effects. Success probability was higher in patients with central NP compared to peripheral NP (OR = 2.03[1.04;4.00]), and among those with central post‐stroke pain, this probability was higher in ischemic versus hemorrhagic strokes (OR = 3.36[1.17;10.05]). PR obtained with iterative rTMS sessions was an excellent predictor of eMCS efficacy. Conclusions While rTMS shows promise as a therapeutic option for some patients with drug‐resistant NP, it does not benefit all patients. Efficacy varies by NP aetiology, aiding patient selection. For responders, eMCS may offer a permanent solution. These findings support a tailored approach to rTMS in NP management, while recognizing both its potential and limitations across diverse patient profiles. Significance Statement Multiple rTMS sessions demonstrate long‐term efficacy and safety in treating drug‐resistant neuropathic pain. Extending session numbers for the test period can enhance responder identification, especially in patients with initial low pain relief. This identification refines patient selection for neurosurgery, reducing non‐responders. Central neuropathic pain shows higher success rates than peripheral. For post‐stroke central pain, patients with ischemic stroke are more likely to respond than those with hemorrhagic stroke. These results support integrating rTMS into clinical practice for managing neuropathic pain.