There was an offhand comment about the Corsair in "The Doctor's Wife", but other than that, I can't think of other established Time Lord characters that have changed gender. Romana, the Doctor and the Master have all remained consistent with their gender.

I mean, it's possible that the Corsair is gender fluid.

And theoretically the Doctor could be gender fluid even though he hasn't been shown to be such up to this point.

But if you think that the Doctor becoming a woman would be anything other than "female body parts = I'm a woman now! LOL BOOBS!" then you're kidding yourself.