Oh! Pretty sure the Sailor Star Lights from the final season of Sailor Moon qualify in some way, and if we're going by the manga/Crystal, then there's a fair amount of evidence for Tenou Haruka as well, IMO.

There's also an old Argentinean cartoon called Cyber Six (very well done, as I recall, though I need to do a rewatch) that might qualify: The title character presents as male for their day job and as female when superheroing. I wanna say it's from the late nineties?

(There is absolutely a case to be made for the main human character of Pixar's Inside-Out, IMO, since every other character in the film has single gender "emotions" that match the gender they present as, but whether that counts as canon I can't say.)