The Difference Between a TMJ Temporor Mandibular Disorder Headache,And A Migraine Headache Written By Donna Lee aka Sugar Plum First here are some similarities between them. 1).Always have a one side of the head type headache where one side is worse than the other side. 2).The same medicine that you take for a migraine headache that helps it can also be taken for a TMJ headache,and can help it as well. 3).Being on the computer can cause either kind of headache. 4).Stress can cause either kind of headache. Here are the differences between them. The one side of your head that hurts it isn't just your head on that side that hurts,it includes your cheek,teeth,neck,back of the head on the side that hurts. That is the only way that I know of where you can actually tell the difference. This comes from my own experience with both kinds of headaches.