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I didn't actually watch either of them, so I don't know how well they fit the description, but the other "magic school" animations from the '00s I'm aware of are Winx Club and Sabrina's Secret Life.
Edited by DaibhidCI remember this show! It focused on a group of girls who went to the school, and it was like Harry Potter because they all had black uniforms and lived in a castle. It was either an all-girls school, or a co-ed that only focused on the female students.
The series started around 2002, as I recall, and came on HBO Family in my house. But I can't for the life of me remember the name of it...
I think you may be thinking of "Creep School", it was a Canadian animation show that aired on Teletoon about four kids (I remember the goth girl was Janice and I think the blonde was Victoria) who accidentally ended up at a school for monsters.
You can't choose what genre your life is, so for the love of God, just be genre savvy.Wait, there is an Animated Adaptation of The Worst Witch?
"And as long as a sack of shit is not a good thing to be, chivalry will never die."

It's an animation show that aired around 2003/2005, probably in Nickelodeon. It was set in a boarding school for magic/school were magical stuff happened; but it didn't feel(too much)like a Harry Potter rip-off. I believe it centered around a group of "normal" students having to deal with this fantastic world. The principal/main teacher was a witch who may have had some sort of weird looking flying pet. Among the main children, there was a blonde rather whiny girl(she also had a weird-looking nose) who had to share the room with a "goth" student (Her hair was black and quite big) who had rapidly adapted to the school. Some of the other students and teachers might have been trolls or different kinds of supernatural creatures. Episodes I remember centered around a student messing with magic they don't understand to deal with a regular problem and learning some sort of lesson. There was an episode in which they were putting up a play and the got possessed by the characters until they finished the play. The opening sequence, as I remember it, showed the characters being dropped off at school, encountering weird stuff, trying to escape while the theme tune narrated the facts and may have said something about these students being mistakenly sent to the school. The show was probably American or Canadian, was traditionally animated and may have been named after the school.