Disclosed is a system and method for treating headaches. The system employs a self-contained, battery operated, readily portable and easy-to-operate head-mounted magnetic depolarizer to generate a transient or time-varying high-intensity magnetic field into and around the user's head or neck. The magnetic depolarizer system can be used to depolarize the neurons of the brain and/or the trigeminal nerve. This type of neuronal depolarization has the capability for terminating migraine or other types of headaches.