It has been studied widely in both research and clinical practice for almost 40 years but most extensively since ~1990 to now. With repetitive TMS (rTMS) there are very small chances of inducing a seizure if say, the patient has temporal lobe epilepsy, but it is generally considered a very safe procedure. And there are well established intensity/repetition frequency limits for such cases defined by stimulation region. It is even done in psychiatric (non-hospital) settings. See chapter 5 for more information: http://erewhon.superkuh.com/library/Neuroscience/Magnetic%20... (Magnetic stimulation in clinical neurophysiology / Mark Hallett and Sudhansu Chokroverty. 2nd ed, 10MB PDF)
I was a research subject for a TMS study a few years ago (I made myself eligible by way of a bicycle accident). Having your thumb twitch because the researcher “shot” magnetic fields at my brain was an amusing experience; she said some people completely freak out at it.