Objective: Phantom limb pain (PLP) is believed to be linked to the reorganization of the deafferented sensory cortex. We present a case of a patient with upper extremity PLP who was successfully treated with repetitive transcranial magnetic stimulation (rTMS). Methods: We treated an active duty service member who suffered an amputation of his right upper extremity after sustaining a blast injury in Afghanistan. He had 28 sessions of alternating sequences of rTMS to the left dorsolateral prefrontal cortex and primary sensory cortex of the left cerebral hemisphere. Pain intensity was assessed with the Visual Analogue Scale. Results: We delivered 1 Hz stimulation to the sensory cortex corresponding to the area of amputation five times a week. After 4 sessions, the patient's pain decreased from a Visual Analogue Scale of 5 to 2. Left 10 Hz stimulation was added and after 28 sessions, the pain decreased from 2 to 1. Conclusions: Our findings support that rTMS was an effective modality for this patient in treating his PLP. The significance of 10 Hz stimulation is unknown because of the lack of an effect size and is possibly associated with a floor effect.