Background: Neuropathic pain is associated with changes in motor cortical representation and corticospinal excitability. Transcranial magnetic stimulation (TMS), a noninvasive method to stimulate the cortex, allows for detailed evaluation of motor cortical function. TMS–based motor mapping offers insights into alterations in motor cortical representations, but their relationship with pain severity remains unclear. Purpose: This study aimed to investigate the correlation between pain intensity and motor cortical representation in individuals with neuropathic pain through TMS motor mapping. Methods: Fourteen patients with chronic neuropathic pain in the upper limbs underwent TMS motor mapping. Parameters measured included resting motor threshold (RMT), mapped area (area eliciting motor evoked potentials ≥50 µV), and Distance50 (distance from the center of gravity to the estimated location of a 50 µV response). The ratio of the affected to unaffected hemispheres (AH/UH) was calculated. Pain intensity was assessed using the visual analog scale (VAS), numerical rating scale, and short–form McGill pain questionnaire 2. Results: A substantial negative correlation was identified between VAS scores and the AH/UH ratio of the map area (rs = –0.68, p = 0.01), suggesting that increased pain was linked to a reduced motor representation in the affected hemisphere. Conversely, no significant interhemispheric variances or associations with pain intensity were noted for the RMT or Distance50. Conclusions: The findings indicate that alterations in corticospinal excitability play a role in the pathophysiology of neuropathic pain. TMS motor mapping holds promise as a valuable biomarker for comprehending the pathophysiology of neuropathic pain and assessing treatment effectiveness.