Does Armour thyroid cause headaches? I had my thyroid removed 7 weeks ago due to a “kissing thyroid and a zillion nodules”, noncancerous. I was put on Levothyroxine but heard great things about Armour Thyroid. Made the switch about 2 weeks ago, but I’ve had a headache everyday getting progressively worse to the point that I have had a migraine for 3 days straight now. It’s gone in the morning until about an hour or so after I take the medicine. I am on Armour Thyroid 90mg. I called my doctor to see if the headaches could be related. Didn’t get to speak to the doc, but to her PA. He shut me down quick and said it couldn’t be related. He wouldn’t tell me anything else other than the headaches are separate from my thyroid medicine for lack of a thyroid. Has anyone else had headaches on the Armour Thyroid? Do they go away eventually?