You mean you want the school itself to have fantasy elements, along the lines of Hogwarts?
The magical school setting is common because it makes sense. Regular kids go to regular school. Why shouldn't magical kids go to a magical school? There's an element of wish fulfillment, too, since a lot of kids wish they were studying spells and potions instead of math and grammar.
Whether or not anyone considers the idea of fantasy schools to be cliched, I don't think these stories will disappear. They're too much fun! It has been done a lot, though, so if you want to stand out, you'll need to put your own unique twist on it. The trick is to make sure your fantasy school story doesn't sound like all the other fantasy school stories out there. Being very familiar with the market and what's already been done will help.