- Newbery Medal for Fiction in 2005 for The Spiderwick Chronicles
- Eisner Award for Best Writer/Artist in 2006 for The Coldest Girl in Coldtown
- Edgar Award for Best Young Adult in 2011 for White Cat
- Nebula Award for Best Novella in 2012 for "The Girl Who Drank the Moon"
- World Fantasy Award for Best Novel in 2019 for The Cruel Prince