Yes. I have no medical conditions and I never have headaches. I am 17 and male. I went to the dentist and got some x-rays and a panoramic of my teeth. Nothing big, but my upper jaw was slightly sore - nothing painful, though. Then, I went to the orthodontist and got a side-view x-ray of the whole head. The scan started at the front and moved toward the back over a period of about ten to twenty seconds. Within a minute or two I had a moderate headache that degraded linearly over the next twenty-four hours. My sister got the same scan and experienced no headache. A few days later, an oral surgeon took a 3D-scan of my jaw, which consisted of a series of x-rays taken at different angles, which is used to make a digital model of my jaw and teeth. No headache this time, although I had a slightly sore jaw again.
Yes, it's weird, and most people don't feel anything.