Some people immediately shout 'Harry Potter,' but that feels almost too obvious, like recommending water for thirst. The school of magic concept has been stretched into some incredible shapes since then. I got completely lost in 'The Magicians' by Lev Grossman—it's like if grad school had existential dread and a Narnia-esque alternate world, but with characters who are deeply flawed and genuinely terrible to each other sometimes. The magic is treated as a rigorous, almost joyless discipline, which is a fascinating and brutal take.
Then there's Naomi Novik's 'A Deadly Education.' It clicked because the school itself is actively trying to kill the students. The protagonist, El, is so prickly and anti-social, a breath of fresh air after decades of chosen ones. The magic system, based on affinities and languages, feels both archaic and weirdly logical. For something lighter but packed with heart, 'The House in the Cerulean Sea' isn't a school story per se, but it's about an orphanage for magical children, and it delivers that found-family-in-a-magical-setting vibe better than anything I've read lately.