| 2024 | Navola | New York Public Library Best Books source ↗ (opens in a new tab) | Selection · Best Books for Adults | |
| 2024 | Navola | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2024 | Navola: A Novel | Chicago Public Library Best of the Best source ↗ (opens in a new tab) | Selection · Must-Read Books: Fantasy, Horror & Sci-Fi | |
| 2019 | The Tangled Lands | World Fantasy Award (Novel, Collection and Anthology) source ↗ (opens in a new tab) | Winner · Collection | |
| 2019 | The Tangled Lands | Locus Awards source ↗ (opens in a new tab) | Finalist · Collection | |
| 2018 | Tool of War | Locus Awards source ↗ (opens in a new tab) | Finalist · Young Adult Book | |
| 2016 | The Water Knife | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2016 | The Water Knife | Locus Awards source ↗ (opens in a new tab) | Finalist · SF Novel | |
| 2015 | The Doubt Factory | Locus Awards source ↗ (opens in a new tab) | Finalist · Young Adult Book | |
| 2015 | The Doubt Factory | Edgar Allan Poe Awards source ↗ (opens in a new tab) | Nominee · Best Young Adult | |
| 2015 | The Water Knife | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Science Fiction | |
| 2015 | The Water Knife: A Novel | NPR Books We Love source ↗ (opens in a new tab) | Selection · Books We Love | |
| 2015 | The Water Knife | Paste Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2015 | The Water Knife | Library Journal Best Books source ↗ (opens in a new tab) | Selection · Genre Fiction | |
| 2014 | Zombie Baseball Beatdown | Locus Awards source ↗ (opens in a new tab) | Finalist · Young Adult Book | |
| 2013 | The Drowned Cities | Locus Awards source ↗ (opens in a new tab) | Finalist · Young Adult Book | |
| 2012 | The Drowned Cities | Los Angeles Times Book Prizes source ↗ (opens in a new tab) | Finalist · Young Adult Literature | |
| 2012 | Ship Breaker | Dublin Literary Award source ↗ (opens in a new tab) | Longlist · Fiction | |
| 2012 | The Drowned Cities | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Teen | |
| 2011 | Ship Breaker | Locus Awards source ↗ (opens in a new tab) | Winner · Young Adult Book | |
| 2011 | Ship Breaker | Michael L. Printz Award source ↗ (opens in a new tab) | Winner · Young Adult Literature | |
| 2011 | The Windup Girl | Dublin Literary Award source ↗ (opens in a new tab) | Longlist · Fiction | |
| 2011 | Ship Breaker | Nebula Award (Novel, Novella and Andre Norton) source ↗ (opens in a new tab) | Nominee · Andre Norton | |
| 2011 | The Alchemist | Nebula Award (Novel, Novella and Andre Norton) source ↗ (opens in a new tab) | Nominee · Novella | |
| 2010 | The Windup Girl | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Winner · Best Science Fiction Novel | |
| 2010 | The Windup Girl | Locus Awards source ↗ (opens in a new tab) | Winner · First Novel | |
| 2010 | The Windup Girl | Hugo Award (book categories) source ↗ (opens in a new tab) | Winner · Novel | |
| 2010 | The Windup Girl | Nebula Award (Novel, Novella and Andre Norton) source ↗ (opens in a new tab) | Winner · Novel | |
| 2010 | Ship Breaker | National Book Awards source ↗ (opens in a new tab) | Finalist · Young People's Literature | |
| 2010 | The Windup Girl | BSFA Awards source ↗ (opens in a new tab) | Shortlist · Best Novel | |
| 2010 | Ship Breaker | Chicago Public Library Best of the Best source ↗ (opens in a new tab) | Selection · Best Teen Fiction | |
| 2010 | Ship Breaker | Publishers Weekly Best Books source ↗ (opens in a new tab) | Selection · Children's Fiction | |
| 2009 | Pump Six and Other Stories | Locus Awards source ↗ (opens in a new tab) | Winner · Collection | |
| 2009 | The Windup Girl | TIME Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2009 | The Windup Girl | Publishers Weekly Best Books source ↗ (opens in a new tab) | Selection · SF/Fantasy/Horror | |
| 2008 | Pump Six and Other Stories | Publishers Weekly Best Books source ↗ (opens in a new tab) | Selection · SF/Fantasy/Horror | |