The Mysterious Benedict Society is an action-adventure, puzzle solving, mystery series (not fantasy), but it is so good, I thought I'd suggest it anyway.
A brief version of the synopsis on Amazon: "After Reynie Muldoon responds to an advertisement recruiting "gifted children looking for special opportunities," he finds himself in a world of mystery and adventure. The 11-year-old orphan is one of four children to complete a series of challenging and creative tasks, (to) become the Mysterious Benedict Society. The four then travel to an isolated school where children are being trained by a criminal mastermind, and the young investigators need to use their special talents and abilities in order to discover his secrets."