Hot answers tagged phrase
I think the colloquial way (and most common way) is: 頭が痛い。 Or even more colloquially dropping が: 頭痛いよ。 Please note that 痛い is an i-adjective so 「頭が痛いだ。」 is not correct. This can be used for other body parts too. I think that the confusion is because in English there are words for some of the "aches" which you often use, like "headache" or ...
You have a couple choices: 頭が痛い （not ×頭が痛いだ） 頭痛がする I basically agree with Szymon's answer that 頭が痛い is more colloquial and all-around more common. You can use either phrase, though. (You can make it more colloquial yet by omitting the particle が.) Adding だ to adjectives like 痛い is nonstandard. To make these more polite, use 頭が痛いです or 頭痛がします.
Only top voted, non community-wiki answers of a minimum length are eligible