The most common side effect related to treatment during clinical trials was scalp discomfort during treatment sessions. This side effect was generally mild to moderate, and occurred less frequently after the first week of treatment. Individuals with migraine headaches tolerate the treatment well and some find their migraine headaches improving as a result of TMS Therapy. If necessary, you can treat this discomfort with an over-the-counter analgesic.

In clinical trials, over 10,000 TMS treatments demonstrated its safety, with no occurrence of seizures. However, there is a small risk of a seizure occurring during treatment, although this risk is no greater than what has been observed with oral antidepressant medications.