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I think you're looking for The Life and Times of Juniper Lee. It was on Cartoon Network from 2005 to 2007. Juniper Lee was like Buffy The Vampire Slayer, but with a Chinese girl, and it was her job to keep the balance between the magical and mortal worlds.
If it's not that then it might be American Dragon Jake Long, which is about a boy who turns into a dragon, and he has a little sister.
Those are the only leads I have. I'm sorry if it doesn't do much help.
It's a good thing our last name isn't Drew, because then you'd be Nancy Drew and I'd be Andrew Drew. -Andy BotwinCould it have been Samurai Girl
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Actually, I think that's it. The movie came out in 2006, but the ad about it was most likely earlier than that, being for an upcoming movie. It doesn't look familiar, but it's got all the right elements. Most importantly, there's a scene where Wendy throws her lipstick through her brother's cookie.

I remember reading about this show in a Disney Adventures magazine in the early 2000's. There's a girl, and she goes to school, but she's also secretly a mystical ninja warrior or something. It mentioned her having a younger brother, wearing a medallion around her neck that protected her, and using her ninja skills for Mundane Utility, like getting to class on time, carrying huge armfuls of books, and knocking a cookie out of her brother's hand from across the cafeteria by throwing a tube of lipstick. (I don't know if she actually did these things in the show.)