As with any medical treatment , rTMS carries a risk of side effects. However,  rTMS is generally well-tolerated and only a small percentage of patients discontinue treatment because of side effects.

You may experience tapping, facial twitching and painful sensations at the treatment site while the magnetic coil is turned on. These types of sensations are reported by about one third of patients. You should inform staff if this occurs. The treatment staff may then adjust the stimulation settings or make changes to where the coil is placed in order to help make the procedure more comfortable for you. In addition, about half the patients treated with rTMS experience headaches. You understand discomfort and headaches tend to get better over time and that the headaches generally responded very well to over-the-counter pain medications.