One of my favorites when I was her age (and continues to be a favorite) is A Wrinkle in Time by Madeline L'Engle. I want to recommend this novel especially because its protagonist is female.
Here's a brief synopsis of the plot.
Meg Murray is sort of a social outcast. She is not terribly interested in the things her peers are interested in. They consider her boring and deliberately exclude her. Meg's younger brother, Charles Wallace, is also an outcast; he is too smart and makes his classmates uncomfortable.
Meg's father is a physicist. He had been working on a very complicated and secretive project called a "tesserat." One day, Mr. Murray disappears. There is gossip all over town that Mr. Murray has left the family for another woman. But Meg steadfastly refuses to believe this is the case.
Meg's suspicions are confirmed when a trio of mysterious women arrive: Mrs. Whatsit, Mrs. Who, and Mrs. Which. They charge Meg, Charles Wallace, and their friend, Calvin O'Keefe with finding Mr. Murray.
The journey will take them to other planets where they battle a shadowy force of evil in order to save their father, and the universe.
Although this is an older work (1962), its themes are timeless.
If your daughter loves a continuing series, this is a great one. There are four other works that follow Meg and Charles Wallace:
I also love A Wrinkle in Time. Fantastic read.
Additional books that many middle schoolers (and high schoolers) love that are fantasy genre (like the Harry Potter series) are The Secrets of the Immortal Nicholas Flamel by Michael Scott. There are currently 5 books in the series. I began the first book, The Alchemyst, upon the recommendation of one of my former students. I'm over halfway through it and I'm anxious to finish it and move on to the next book.
Also, if you have not yet heard of them, there's the Hunger Games Trilogy by Suzanne Collins. This is an incredibly popular science fiction/fantasy trilogy. Lots of action, intrigue and some romance.
I am and have always been a huge reader and the Harry Potter series captured me in elementary. Some books I liked very the Lord of the Rings and the Hobbit, the Hunger Games is great, Eragon was a good book and series, if you want some mystery I would also suggest Nancy Drew or the Hardy Boys. Also here are two series I simply love as well, The Guardians of Ga'Hoole (this was one that captured my attention in elementary and I was always excited to read a new one) and The Secrets of the Immortal Nicholas Flamel. Personally I thought those were all interesting and I have more but I'll stick with this for now, in general I am a huge reader.
Fantasy lovers enjoy the Tolkien books (Lord of the Rings, The Hobbit, etc). Do not assume she will love the Hunger Games just because its gaining popularity. The Hunger Games is part of a new kind of sci fi that is more teen romance / chicklit than fantasy or sci fi.