Using functional MRI (fMRI) we investigated 13 upper limb amputees with phantom limb pain (PLP) during hand and lip movement, before and after intensive 6-week training in mental imagery. Prior to training, activation elicited during lip purse showed evidence of cortical reorganization of motor (M1) and somatosensory (S1) cortices, expanding from lip area to hand area, which correlated with pain scores. In addition, during imagined movement of the phantom hand, and executed movement of the intact hand, group maps demonstrated activation not only in bilateral M1 and S1 hand area, but also lip area, showing a two-way process of reorganization. In healthy participants, activation during lip purse and imagined and executed movement of the non-dominant hand was confined to the respective cortical representation areas only. Following training, patients reported a significant reduction in intensity and unpleasantness of constant pain and exacerbations, with a corresponding elimination of cortical reorganization. Post hoc analyses showed that intensity of constant pain, but not exacerbations, correlated with reduction in cortical reorganization. The results of this study add to our current understanding of the pathophysiology of PLP, underlining the reversibility of neuroplastic changes in this patient population while offering a novel, simple method of pain relief.