| 2025 | When We Were Real | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2022 | Revelator | Locus Awards source ↗ (opens in a new tab) | Finalist · Horror Novel | |
| 2022 | The Album of Dr. Moreau | Edgar Allan Poe Awards source ↗ (opens in a new tab) | Nominee · Best Paperback Original | |
| 2021 | Revelator: A Novel | New York Public Library Best Books source ↗ (opens in a new tab) | Selection · Best Books for Adults | |
| 2018 | Spoonbenders | Locus Awards source ↗ (opens in a new tab) | Finalist · Fantasy Novel | |
| 2018 | Spoonbenders | Nebula Award (Novel, Novella and Andre Norton) source ↗ (opens in a new tab) | Nominee · Novel | |
| 2018 | Spoonbenders | World Fantasy Award (Novel, Collection and Anthology) source ↗ (opens in a new tab) | Nominee · Novel | |
| 2017 | Spoonbenders: A Novel | NPR Books We Love source ↗ (opens in a new tab) | Selection · Books We Love | |
| 2016 | Harrison Squared | Locus Awards source ↗ (opens in a new tab) | Finalist · Young Adult Book | |
| 2015 | Afterparty | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2015 | Afterparty | Lambda Literary Awards source ↗ (opens in a new tab) | Finalist · Science Fiction/Fantasy/Horror | |
| 2015 | We Are All Completely Fine | Nebula Award (Novel, Novella and Andre Norton) source ↗ (opens in a new tab) | Nominee · Novella | |
| 2014 | We Are All Completely Fine | Shirley Jackson Awards source ↗ (opens in a new tab) | Winner · Novella | |
| 2014 | Afterparty | NPR Books We Love source ↗ (opens in a new tab) | Selection · Books We Love | |
| 2014 | Afterparty | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2011 | Raising Stony Mayhall | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Horror | |
| 2011 | Raising Stony Mayhall | Library Journal Best Books source ↗ (opens in a new tab) | Selection · SF/Fantasy | |
| 2011 | Unpossible | Publishers Weekly Best Books source ↗ (opens in a new tab) | Selection · SF/Fantasy/Horror | |
| 2010 | The Devil's Alphabet | Philip K. Dick Award source ↗ (opens in a new tab) | Nominee · Paperback Original | |
| 2009 | Pandemonium | Mythopoeic Fantasy Awards source ↗ (opens in a new tab) | Finalist · Adult Literature | |
| 2009 | Pandemonium | Locus Awards source ↗ (opens in a new tab) | Finalist · First Novel | |
| 2009 | Pandemonium | World Fantasy Award (Novel, Collection and Anthology) source ↗ (opens in a new tab) | Nominee · Novel | |
| 2009 | The Devil's Alphabet | Publishers Weekly Best Books source ↗ (opens in a new tab) | Selection · SF/Fantasy/Horror | |
| 2008 | Pandemonium | Shirley Jackson Awards source ↗ (opens in a new tab) | Finalist · Novel | |