My teenage son SWCAH has suffered all his life from headaches. We were told that it was nothing to do with CAH but now the endo has said after extensive blood work that low cortisol levels are certainly a contributing factor. I recently went to a conference and an adult endo said that anyone on cortisol replacement therapy is prone to have headaches, over treatment as well as under treatment can cause these.  I was shocked by the amount of people who raised their hands when the subject brought up.  Dehydration can also cause headaches!