Can headaches be a herx?

Yes headache can be definitely sign of herx. I had therrible headaches after starting ATB. And also when it is after 2 weeks, it is possible.

Yes it can, but a herx isn't a good thing. A herx is oxidative stress and oxidative stress with free radical production is detrimental to good health. We often use a herx as a signal that we are progressing, but in a perfect world, we progress without a herx. Our inability to methylate and detox efficiently is what causes the immunopathology.