If you are using your iPhone (or any phone for that matter) during long periods of time (>5") several times per day, a bluetooth adaptor would work in your favor. They are cheap and will prevent your headaches. For the cost of a GP/MD visit, you will pay for your bluetooth.
Part of the problem is the amount of pressure applied to the auricle (outer ear) and tilt of the head during extended cell phone usage. An example, take your iPhone, while it's turned off, and place next to your ear for about 20-30". Notice anything??? Pain, continue, and it will become increasingly uncomfortable (causing the headache). Older landline telephones would essentially give anyone a headache if you kept the phone on one ear, after about 15-20 minutes of talking, tilting the head, trying to multitask, although they were not nearly as warm.
A good bluetooth is my Rx for you. Good luck and keep us up2date.