There are so many great Middle Grade fantasy series out there for boys:
Artemis Fowl Series by Eoin Colfer (2001-current)
Spiderwick Chronicles by Tony DiTerlizzi and Holly Black (2003-2004)
Percy Jackson and the Olympians by Rick Riordan (2005-2009)
Fablehaven Series by Brandon Mull (2006-current)
There are also a lot of YA "girl" fantasy books teenage boys would like if they gave them a change:
Will of the Empress by Tamora Pierce (2005)
Peeps Duology by Scott Westerfeld (2005-2006)
Wake Series by Lisa McMann (2008-2010)
Graceling Series by Kristin Cashore (2008-current)
Voices of Dragons by Carrie Vaughn (2010)
But the fact is, boys stop reading "kid" books once they get to high school. So many publishers disguise young adult fantasy by publishing it for adults and then marketing it to teenage boys. Don't believe me that many YA fantasies are masquerading as adult fantasies? One of the most common themes in fantasy is a coming-of-age journey that exposed the protagonist to the world:
The Authurian Saga by Mary Stewart (1970-1995)
Xanth Books by Piers Anthony (1977-current)*
Shannara Series by Terry Brooks (1977-current)*
Wheel of Time Series by Robert Jordan (1990-current)*
Stardust by Neil Gaiman (1998)
While this might be a financial decision for publishers (adult books sell way better than YA lit), the outcome isn't negative. It bridges that no-mans land between ages 16 and 21 where a lot of boys stop reading, and it opens deserving books to a larger market of readers.
Very few authors are able to break the mold and write fantasy books published in the YA market both girls and boys enjoy. To those brave authors, agents, editors and publishers, I stand and applaud:
The Earthsea Cycle by Ursula K. Le Guin (1968-2003)
Discworld Novels by Terry Pratchett (1983-current)*
The Heir Chronicles by Cinda Williams Chima (2006-current)
And I can't think of any more past those three, but I welcome your suggestions.
*There are like a gazillion books in these series, so I've only included the first two and the last two.