| Work | Year & Award | Category | Result | Ref. |
| Better Than Home | 2000 A. E. Coppard Long Fiction Prize | | Won | |
| My Father's Mask | 2005 International Horror Guild Award | Intermediate Form | Nominated | |
| Voluntary Committal | 2005 International Horror Guild Award | Long Fiction | Nominated | |
| 2006 Locus Award | Novella | Nominated | |
| 2006 British Fantasy Award | Novella | Nominated | |
| 2006 World Fantasy Award | Novella | Won | |
| 20th Century Ghosts | 2005 International Horror Guild Award | Collection | Won | |
| 2005 Bram Stoker Award | Fiction Collection | Won | |
| 2006 Locus Award | Collection | Nominated | |
| 2006 British Fantasy Award | Collection | Won | |
| 2006 Crawford Award | New Fantasy Writer | Won | |
| 2006 World Fantasy Award | Collection | Nominated | |
| 2008 Audie Awards | Short Stories or Collections | Won | |
| 2010 Tähtifantasia Award | | Nominated | |
| Best New Horror | 2005 Bram Stoker Award | Long Fiction | Won | |
| 2006 Locus Award | Short Story | Nominated | |
| 2006 British Fantasy Award | Short Story | Won | |
| 2006 World Fantasy Award | Short Fiction | Nominated | |
| The Black Phone | 2005 British Fantasy Award | Short Fiction | Nominated | |
| You Will Hear the Locust Sing | 2005 British Fantasy Award | Short Fiction | Nominated | |
| Heart-Shaped Box | 2007 Bram Stoker Award | First Novel | Won | |
| 2007 Bram Stoker Award | Novel | Nominated | |
| 2007 Black Quill Award | Dark Genre Novel (Reader's Choice) | Won | |
| 2008 Macavity Awards | First Mystery Novel | Nominated | |
| 2008 Locus Award | First Novel | Won | |
| 2008 British Fantasy Award | August Derleth Award | Nominated | |
| 2008 Audie Awards | Thriller or Suspense | Won | |
| 2008 International Thriller Writers Award | First Novel | Won | |
| Thumbprint | 2007 Shirley Jackson Award | Novelette | Nominated | |
| 2008 British Fantasy Award | Short Fiction | Nominated | |
| Locke & Key (with Gabriel Rodriguez) | 2008 Rondo Hatton Classic Horror Award | Best Horror Comic Book | Honorable Mention | |
| 2009 Eisner Awards | Best Writer | Nominated | |
| 2009 British Fantasy Award | Comic/Graphic Novel | Won | |
| 2011 Eisner Awards | Best Writer | Won | |
| 2012 British Fantasy Award | Comic/Graphic Novel | Nominated | |
| 2015 Mythopoeic Awards | Adult Literature | Nominated | |
| 2016 Audie Awards | Original Work | Nominated | |
| Gunpowder | 2009 British Fantasy Award | Novella | Nominated | |
| Bobby Conroy Comes Back from the Dead | 2010 Tähtifantasia Award | | Nominated | |
| Horns | 2010 Bram Stoker Award | Novel | Nominated | |
| 2011 RUSA CODES Reading List | Horror | Shortlisted | |
| 2011 Locus Award | Fantasy Novel | Nominated | |
| The Cape | 2011 Eisner Award | Single Issue/One-Shot | Nominated | |
| Locke & Key: Keys to the Kingdom : Sparrow | 2011 Eisner Awards | Single Issue/One-Shot | Nominated | |
| Locke and Key, Vol. 4: Keys to the Kingdom (with Gabriel Rodriguez) | 2011 Goodreads Choice Awards | Graphic Novels & Comics | Nominated | |
| 2011 Bram Stoker Award | Graphic Novel | Nominated | |
| 2012 Hugo Award | Graphic Story | Nominated | |
| 2012 British Fantasy Award | Comic/Graphic Novel | Won | |
| Locke & Key: Guide to the Known Keys | 2012 Eisner Awards | Single Issue/One-Shot | Nominated | |