Magical School Books Not Written By an Evil TERF
Children of the Red King series by Jenny Nimmo
Trans Wizard Harriet Porber series by Dr. Chuck Tingle
Earthsea Cycle series by Ursula K. Le Guin
Circle of Magic series by Tamora Pierce
The Numair Chronicles by Tamora Pierce
The Kingkiller Chronicles by Patrick Rothfuss
The Scholomance Trilogy by Naomi Novik
The Poppy War series by R.F. Kuang
The Magicians by Lev Grossman
The Black Magician Trilogy by Trudi Canavan
Mother of Learning series by Domagoj Kurmaić
Naruto by Masashi Kishimoto (I'm counting it and you can't stop me)
Simon Snow Trilogy by Rainbow Rowell
The Atlas Series by Olivia Blake
The Legendborn Cycle series by Tracy Deonn
The School for Good and Evil series by Soman Chainani
The House in the Cerulean Sea by T.J. Klune
Supernatural Investigations series by B.B. Alston
In Other Lands by Sarah Rees Brennan
Book of the Ancestor Trilogy by Mark Lawrence
Magic for Liars by Sarah Grey
A Wizard’s Guide to Defensive Baking by T. Kingfisher
The Empyrean series by Rebecca Yarros
The Medoran Chronicles by Lynette Noni
Heir Chronicles by Cinda Williams Chima
Summoner Series by Taran Matharu
Vampire Academy series by Richelle Mead
The Black Witch Chronicles by Laurie Forest
The Library at Mount Char by Scott Hawkins
Vita Nostra by Marina and Sergey Dyachenko
Supernatural Beasts and Bullies series by Caroline Peckham and Susanne Valenti
The Culling Trials series by K.F. Breene and Shannon Mayer
Zero Sight series by Justin Shier
Hex Hall by Rachel Hawkins
Roses and Rot by Kat Howard
House of Night series by P.C. and Kristin Cast
The Worst Witch series by Jill Murphy
School for Unusual Magic series by Liz Montague
Alex Stern series by Leigh Bardugo
Note that this is not a full list. If you have other magic school books to recommend, feel free!
Also note that these are only magic school books. There are plenty of amazing fantasy books not set in magical schools, such as Lindsey Byrd's The Sun Blessed Prince or Saara El-Arifi's Faebound.