At least 90% of individuals of limb amputees experience phantom limb pain (PLP). Recent clinical research suggests that providing patients with the mirror image representation of the amputated limb may alleviate PLP. However, mirror therapy cannot be used with bilateral amputees, as visual feedback is dependent on the movement of the intact limb. To overcome this limitation, we designed a novel myoelectric-controlled virtual reality (VR) system for the treatment of phantom limb pain in trans-radial upper extremity amputees. The proposed system allows the patient to directly control the virtual limb by recognizing stump muscle patterns recorded with EMG sensors. The hypothesis behind this strategy is that the VR image of the amputated limb induces better limb imagery than the reflected image of their intact limb and, therefore, is more effective in reducing PLP. A research protocol to test this hypothesis is described.