While countless run-of-the-mill anime schools exist where the protagonist sits by the window in the back of the classroom and magically never does homework, there are some notable exceptions to this rule. A few bizarre anime schools fall under the tyranny of despotic student councils who may or may not use your life essence to feed clothing from space.
These schools might not offer a typical education, but what they lack in algebra classes they make up for with a wholly unique classrooms unlike any you've ever seen before. No, you probably won't learn the basics of surviving the real world, but who needs education when you can learn from the best high school anime out there?
One of the teachers at Kunugigaoka Middle School of Assassination Classroom, Koro-sensei, is literally consists a tentacle and a smiley-face head. Koro-sensei, which translates to "unlikeable teacher," claims to have blown up the moon and will soon follow that up with the Earth itself, unless a specific group of middle school students (who he will spend the year teaching) can assassinate him first.
The school runs on a model of 95% productivity, 5% laziness, with the 5% comprised of the lowest-scoring students. This class is undesirable, ensuring that students strive for their best in order to avoid an E class distinction. Not exactly a standard curriculum, but at Kunugigaoka you learn the basics of assassination alongside mathematics and social studies.
Soul Eater's Death Weapon Meister Academy offers an unusual curriculum. The school (run by Death itself) raises scythes for Shinigami to wield against a wide variety of evildoers. Instead of physical objects, these Scythes are actually humanoid students who transform into weapons at will.
At the academy, Scythes pair up with Shinigami to help them collect the 99 evil souls and one witch soul needed to achieve their Death Scythe potential.
In the world of My Hero Academia, 80% of the population boasts a "quirk" or a superpower. Some use these abilities to become crime-fighting heroes. To do that, they need a proper education, available to them through UA High School.
At UA High, kids develop their quirks, train in methods of combat, and learn to rescue civilians from dangerous situations. A highly selective school with a rigorous curriculum, UA High features some of the world's most accomplished (ridiculous) hero training courses, some of which feature giant robots.
Kids in the Naruto-verse don't go to school to learn about math, science, history, or how to read and write. Or if they do, most of that takes place off-screen. Instead, viewers watch a bunch of children learn to fight with kunai and ninja stars, defy gravity by channeling chakra into their feet, and master the art of hand-to-hand combat.
After students graduate from Ninja Academy, they divide into groups of three and get assigned a teacher, a working ninja who helps bring out their full potential.