This study deals with the diagnostic value of functional magnetic resonance imaging (fMRI) in a patient with phantom limb pain following traumatic amputation of the right arm. After failure with medication, resection of stump neurinoma, and spinal cord stimulation, fMRI with evidence of cortical reorganization was performed. Tactile stimulation of the perioral region and motor imagery with cranial, tactile stimulation of the stump led to a caudal shift in fMRI activity. Subsequent motor cortex stimulation brought relief from the pain. By detecting cortical reorganization, fMRI contributes to the indication for motor cortex stimulation for phantom pain and aids in electrode positioning.