Allodynia, pain caused by innocuous stimuli, is a hallmark symptom of neuropathic pain. Since this symptom is resistant to existing analgesics, it is important to elucidate its underlying mechanism that provides a clue for developing novel therapies. Pain information in the spinal dorsal horn (SDH) is strongly controlled by top-down signals from the brain. While the brainstem is a well-known region of this control, but little is known about the role of other regions. In this study, we comprehensively explored the brain regions with neurons that directly project to the SDH using a whole-brain imaging system. Among many brain regions identified, we examined the role of some regions in neuropathic allodynia and found that activation and inhibition of the rostral ventromedial medulla (RVM)-SDH and primary somatosensory cortex (S1)-SDH neural pathways, respectively, attenuated behavioral response related to allodynia after nerve injury. Furthermore, inhibition of the S1-SDH pathway also reduced the number of c-FOS-positive neurons in the superficial lamina in SDH in response to optogenetic stimulation of primary afferent Aβ fibers. These data indicate the importance of these top-down signaling pathways in neuropathic allodynia and propose that these pathways may be therapeutic targets for neuropathic pain.