Marvel 2099 had a Superhero Orphanage: the Xavier Shelter for Indigent Children in X-Nation 2099.The French comic Freaks' Squeele revolves around the students' life in a university for heroes, specialized in (pretty lame) bad guys and villains.Pride High has this as its core premise: a gay/straight alliance at a superhero high school.In this case he's the odd one out for wanting to be a hero, in spite of his powerlessness the other kids might be the children of superheroes and have abilities of their own, but in general they aren't interested in running off to try and save the world once they've graduated - most of them want to use their powers in the most self-serving way possible, and three in particular want to be villains! The mini-series Grounded follows the only normal kid in the school for superpowered teens.Courses include Secret Identities (taught by an obvious analogue of Superman, right down to the glasses) and Morality (the instructor of which had over 32 confirmed kills in the Dark Age).

The Seminary in The Intimates, where powered teens are sent by their stage parents to develop skills they wish they didn't have.

Hero Camp is sort of like this, but, you know, summer camp instead of an actual school.

In an upcoming arc, they are moving the academy to the old West Coast Avengers compound and adding a bunch of other teen heroes as students.

Initiative's successor Avengers Academy is a more traditional example, except it's more about training kids so they wouldn't become supervillains.

The Avengers' Initiative program is somewhat like this, but blurs the line heavily between 'school' and 'boot camp.' Not many other examples listed here take young teens and put sniper rifles in their hands.

They've also implied the existence of a good counterpart.

The comic Necessary Evil has the eponymous Supervillan School.

The Legion Academy from The Legion Of Super-Heroes.

The manga-inspired French comic book Sentai School.

And the Praetorian Academy, PS238's rival which is heavily troped to be a supervillain school: you've got your Evil Headmaster, your Military Discipline, your Faceless Minion Masks, your overly-militaristic student codenames, and of course the overwhelming arrogance that they are far superior to their rival school.

The fallout of the Schism storyline has Wolverine establishing the Jean Grey Institute for Higher Learning, largely featuring students from the now-defunct Xavier Institute.

It got to the point where Xavier's 'school' was so chock-full of adult superheroes that they changed the name from Xavier's School for Gifted Youngers to the Xavier Institute for Higher Learning, making it a superhero college, and opened a franchise with the formerly evil rival Massachusets Academy for Generation X.

Xavier's school now has a lot of non-superhero mutants of all ages, learning to control their powers as well as reading, writing, and 'rithmetic. The films cemented the concept in people's minds though, and the ComicBooks followed suit.

In fact, the Xavier Academy jumped around a bit between being a Super-Hero School, and a superhero base which happened to be disguised as a school, largely because, until Kitty Pryde joined the Chris Claremont 'all-new all-different' X-Men's ages ranged from the 20's onwards, with none of them even of college age.

Depending on the continuity, Emma Frost's school, the Massachusetts Academy, may count as a supervillain school if she is Xavier's foe.

The Trope Maker is Professor Charles Xavier's school in X-Men.

While the 'hero' part is debatable, it's a school for people with powers, most of which easily qualify as 'super'.

Academy City in A Certain Magical Index is dedicated to the study and development of psychic powers, with students who have undergone the development program comprising the vast majority of the population.

To an extent, Duel Academia in Yu-Gi-Oh! GX-at least, it was designed specifically to train duelists strong enough to defend three dangerous forbidden cards from falling into the wrong hands, and it's a Weirdness Magnet for kids with the power to communicate with spirits from another world.

Examples of Super-Hero School include: Anime and Manga

Super hero academy in stories