The management of higher brain dysfunctions such as stroke-induced unilateral spatial neglect (USN) or aphasia is crucial because these dysfunctions have devastating neurological repercussions on the patients' daily life and quality of life. Impairment of the physiological interhemispheric rivalry is often the result of brain insults such as strokes or traumatic injuries, and it may lead to USN or aphasia. Repetitive transcranial magnetic stimulation (rTMS), a non-invasive brain stimulation method, is a promising tool for restoring the pathological imbalance in interhemispheric rivalry by either suppressing the hyperactivity of the unaffected hemisphere or facilitating hypoactivity in the affected hemisphere. The concept of paradoxical functional facilitation (Kapur, 1996) has important clinical implications when coupled with rTMS applications. In addition to conventional rTMS (c-rTMS), other clinically relevant protocols of patterned rTMS (p-rTMS) have been developed: the theta burst stimulation (TBS), the paired associative stimulation (PAS), and the quadripulse stimulation (QPS). TBS is commonly used in the rehabilitation of patients with post-stroke USN and those with non-fluent aphasia because of its prolonged beneficial effects and the short duration of stimulation. TBS may be considered an effective and safe protocol of rTMS. We foresee broader clinical applications of p-rTMS (TBS) and c-rTMS in the treatment of various neurological deficits.