Tallulah - what sort of books does he enjoy, if not fantasy? There is a lot of good fantasty fiction out there at the moment, but there's other stuff around too. The following spring instantly to mind:
Eoin Colfer: Artemis Fowl is quite unusual.
Marcus Sedgwick: The Dark Horse is one of the best children's books I've read this year.
Fighting Fantasy books are very popular with this age group too. If you haven't got any of these The Book People have got a very good offer at the moment - 10 for £9.99.
What else? Philip Reeve's Mortal Engines won the Blue Peter book prize recently for the most unputdownable book.
Mark Haddon's Curious incident of the dog ... would be something quite different, but I think would grip a 12 yr-old.
OK I'm finding it very hard to stop here.
Yann Martel's Life of Pi is amazing, and highly entertaining. Not what I was expecting at all.
These are what instantly spring to mind as definite successes, but not in the HP/LotR mould. If these don't appeal, why not post a few of examples of the sort of thing he has enjoyed reading, and we can try and make some more tailored suggestions.
HTH