I'm a bit surprised that no one has mentioned Tamora Pierce's assorted books. Probably the best known are the Song of the Lioness series and Protector of the Small series. She also has a number of other books, some set in the same world, others not.
The Artemis Fowl stories by Eoin Colfer are modern fantasy and might appeal to him. Let's face it the idea of a 12 year old as an evil genius has to appeal to any 11 year old boy.
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