Repetitive transcranial magnetic stimulation (rTMS) is a non-invasive method for treating various neurological and psychiatric disorders. With the growing demands of neuropathic pain patients and their increasing numbers, rTMS treatment tools are becoming more necessary. rTMS uses electromagnetic induction to induce weak electric currents by rapidly changing the magnetic field. Targeting the electric current to a specific part of the brain is one treatment for pain relief. This paper focuses on treatment for neuropathic pain caused by a lesion or disease of the central or peripheral nervous system, including stroke, trauma, or surgery. However, the current style of rTMS treatment is still developing and is so technically specialized that only a limited number of hospitals and only a handful of specialists can provide this therapy. The existing rTMS systems use an optical markerbased 3D sensing technique that positions the stimulation coil to target the small region of interest in the brain through coregistration with pre-scanned MRI data. This system requires the patient to be immobilized on a bed. The optical markers for 3D sensing are placed on the patient's head to maintain accurate positioning. We propose a constraints-free, markerless rTMS system, which employs ego-motion, a computation technique to estimate relative 3D motion of a camera to what the camera sees. We use a ToF sensor as a camera, which is capable of capturing shape information from a single viewpoint instantly. The markerless target spot is based on the shape features of the patient's face. This paper shows the process of a prototype system and its potential for achieving an easy-to-handle system framework.