Our daughter had this symptom. It wasn't a headache, but a pain in her skull bone, always in one spot (for her it was just behind the right ear, but closer to the top of her head). Quick and then gone. I would assess this symptom level by number of times it occurred during the day, not by intensity, because it always seemed intense.
Because this was one of her bone pains (shin, forearm as well) which flared during bartonella abx treatment herxes we have always assumed it to be caused by bartonella. We even call this her "bartonella spot".
This pain has resolved with treatment.