In Ranma ½, Sparkling Generation Valkyrie Yuuki, Abstract Gender and Misfile, a boy finds himself magically transformed into a girl. In both The Wotch and El Goonish Shive, the cast includes a boy who sometimes becomes a girl for a lark. A number of webcomics including Venus Envy are about boys who yearn to become girls.
Are there no cartoons about girls becoming boys?
(See also.)
Also SailorSun and Jeanie Bottle (by the same author).
Also Angels and Aliens, published in both English and (imperfect) Esperanto.
Here’s one: Better Boyfriend.
In Narbonic, Helen flipped herself as well as Dave.
I don’t know yet what Girl Today Boy Tomorrow is about …
My bestie doesn’t know I’ve turned into a girl