There's a subreddit called /r/rational which discusses and shares "rational" and "rationalist" fiction. Many of these include EA themes, both explicitly and implicitly.
Some I'd recommend along with the ones others here have already shared include Worth the Candle, an original fiction about a teenager who gets transported into a fantasy world of his own creation and has to overcome personal challenges like grief and societal ones like complex coordination problems, Animorphs: The Reckoning, a fanfic that re-imagines the alien-body-snatchers story of the original through a much more serious and thoughtful lens, and my own fanfic, Pokemon: The Origin of Species, which explores the pokemon world from a more rational/EA lens while also teaching some psychology and therapy.
There's also comics like Strong Female Protagonist, which is about a superheroine who quits fighting crime and goes to college because she realizes she doesn't know how to "actually" save the world.
There is Eliezer Yudkowsky's Harry Potter fan fiction "Harry Potter and the Methods of Rationality" (HPMOR), which conveys many ideas and concepts that are relevant to EA: http://www.hpmor.com/
Please note that there is also a fan-produced audio version of HPMOR: https://hpmorpodcast.com/
I also really enjoyed the unofficial sequal, Significant Digits. http://www.anarchyishyperbole.com/p/significant-digits.html