Therapeutic applications of repetitive transcranial magnetic stimulation (rTMS) have long been awaited for not only neurological but also psychiatric disorders as a low-invasive transcranial brain stimulation. In 2008, the Food and Drug Administration (FDA) of the United States finally approved repetitive transcranial magnetic stimulation (rTMS) for medication-resistant patients with major depression. More recently, at the beginning of 2013, a deep TMS device with the H-coil received FDA approval as the second TMS device for major depression. In Japan, it is estimated that more than 200,000 patients with medication-resistant major depression could be candidates for rTMS treatment. To promote the clinical introduction of rTMS for major depression, joint discussion has been ongoing including the Japanese Society of Psychiatry and Neurology (JSPN), the Japanese Ministry of Health, Labour, and Welfare (MHLW), and the Pharmaceutical and Medical Devices Agency (PMDA). On the other hand, some corporate efforts have begun to get MHLW/PMDA approval for a few types of rTMS device. In 2013, the JSPN established a new committee in order to discuss the introduction of neuromodulation methods such as rTMS in Japan. The committee has been discussing how rTMS should be introduced appropriately with expedition, considering the MHLW regulations for the expedited introduction or provisional use of advanced medical technology. Also, the MHLW has required related psychiatric societies to formulate clinical guidelines of rTMS for major depression in order to avoid any potential overuse or misuse. A number of controversies are ongoing, such as standards for the appropriate clinical application of rTMS, a suitable position of rTMS within the comprehensive treatment algorithm of major depression, and bioethical standards for brain stimulation (neuroethics). Moreover, there are some pragmatic issues. For instance, the Japanese Society of Clinical Neurophysiology (JSCN) has restricted repetitive TMS administration to medical doctors due to safety concerns. In order to disseminate rTMS in Japan, it should be discussed how to reduce the work-load of psychiatrists who administer rTMS on a daily basis. For this purpose, standards should be established by the JSCN to qualify non-MD rTMS operators under the supervision of psychiatrists. In this paper, recent progress in the clinical introduction of rTMS for major depression in Japan is reported, in order to facilitate future discussion about how rTMS should be introduced for patients with major depression in Japan.