Stranger in a Strange School

By mistake or some odd chain of events, an Ordinary High School Student winds up attending an Extranormal Institute. Perhaps they're a human in an All Ghouls School, or a Muggle in a Wizarding School, but whichever it is, they clearly don't fit in. If the Masquerade is in full effect, they'll probably have to try to blend in with the usual type of student, with the consequence of failure ranging from Laser Guided Amnesia to Cruel and Unusual Death to uphold the masquerade.

Acts as a Naive Newcomer. After sufficient experience, they may upgrade to something that does fit in.

Anime and Manga

 * Mx 0: After failing to sneak into (unknown to him) a secret Wizarding School, Taiga gets dragged though the school's barrier by a teacher mistaking him for a student trying to sneak out. A sequence of unlikely events establishes him as a genius mage when he actually has no power at all--a reputation he is forced to uphold thereafter.
 * Rosario to Vampire: Tsukune accidentally gets accepted to All Ghouls School in Another Dimension and faces the death penalty for spying if discovered.
 * Animal Academy / Hakobune Hakusho: A Book Dumb girl is mistakenly accepted to a school for animal shapeshifters and begs her way in (still not knowing what the school was) when the head faculty see that she's human because no other school will take her. The other students believe she's a cat, because her given name is--quite conveniently (and probably why she was first accepted)--Neko.
 * Kanokon is a borderline case, since the school is dedicated to rehabilitate youkai who have trouble integrating into human society, but at least some unwitting humans attend as well to provide an incentive to be more stealthy about their true natures.
 * Hollow Fields: Lucy Snow is a fairly ordinary child in a school for the children of mad scientists.
 * Inverted in School Shock (and for that matter, Full Metal Panic) where a Child Soldier gets sent to school for a observation and protection mission. Hilarity Ensues.
 * Afterschool Charisma: Shiro's the only non-clone in a school for clones.
 * Sayonara Zetsubou Sensei: Nami Hitou, the normal girl in a Dysfunction Junction class.
 * Ironically, she develops a complex about it, making her Not So Above It All.
 * Ouran High School Host Club is a non-supernatural example: Haruhi is a middle-class girl at a school for the comically rich.
 * And unusual in that as the story starts, she's already attending and has blended in so well that nobody's really noticed her yet.

Comics

 * Angela, the protagonist of The Underburbs and her admirer, George, for entirely different reasons. (Angela has actually gotten turned into a witch by the time she enrolls a short time before.)
 * The strip Strange Hill in The Beezer was a variation--an ordinary teacher stuck in a horror-themed school. On one occasion he was delighted when an apparently normal boy joined his class, but he turned out to be a Mad Scientist.

Film

 * The protagonist of Sky High is a regular boy who gets sent to a Superhero school despite having no powers.

Literature

 * The entire plot of Vampire High is that Cody, as a newcomer to a small town in Massachusetts, is one of the few people unaware that there are vampires living there as well. As a result, he has no idea that the high school he attends is primarily intended for vampires (there are a few humans, but all are there through necessity and not choice).

Live Action TV

 * Inverted in Kyle XY, when the very abnormal Kyle ends up attending the very normal Beachwood High School.

Web Comics

 * Tyler Marlocke of PS 238 - normal, unpowered child in a school for superkids. He doesn't pretend to be anything else, but between the fact that both his parents are legendary superheroes and the school being a constant Weirdness Magnet, he has no choice but to become an Action Survivor in order to, well, survive. Currently in training to become Badass Normal.
 * A-san of Overlord Academy is an accidentally transferred into the titular school. He's an oboist.
 * Graham in Wizard School is a rich, drunken jerk who replaces the "Chosen One" at a school for wizards.

Western Animation

 * My Gym Partners a Monkey is about a human boy accidentally sent to an animal school.
 * Mini Monsters (aka Camp Mini-Mon) had two normal kids accidentally be sent to a Summer Camp for Movie Monsters' (Dracula, Frankensteins Monster, etc.) kids.
 * Similarly, Gravedale High featured Rick Moranis as the only human teacher at an All Ghouls School.