One possibility is sinus barotrauma, although CO2 retention is high on the differential. Since g1138 and TSandM discussed the CO2 headache, I'll expand a little on sinus barotrauma...
As you know, even a little stuffiness or minor barotrauma can inflame the sinus membranes and impair equalization. It would be interesting to ask your friend a few more questions, e.g., specifically when did the headache occur (during descent/at depth/ascent/post-dive), what is the exact location of the pain (entire head isn't specific enough), what is the quality/character of the pain, does ascending/descending alleviate the pain to a certain extent, etc.
FYI, sinus barotrauma most often affects the frontal sinuses, but it can also involve the ethmoid or maxillary sinuses. If sinus barotrauma is the culprit, then your friend could do a couple of things to help avoid such headaches in the future. First, it would be important to descend slowly and avoid any significant down-up-down movement in the water column. Second, it might be helpful to try a long-acting decongestant. Allergy sufferers might find that a saline nasal rinse or regular dosing of an antihistamine can help.
If your friend is curious, he should see a dive-savvy ENT for a comprehensive evaluation. Divers Alert Network should be able to give him a referral. Your friend should expect to answer a lot of the above questions...and more.