| Work | Year & Award | Category | Result | Ref. |
| The Thomas Berryman Number | 1977 Edgar Allan Poe Award for Best First Novel | | Won | |
| Sam's Letters to Jennifer | 2005 Audie Awards | Romance | Nominated | |
| Maximum Ride: School's Out Forever | 2008 Hampshire Book Awards | Book Award | Nominated | |
| Maximum Ride: The Angel Experiment | 2008-2009 South Dakota Library Association | SD Teen Choice Book Awards | MS Winner | |
| 2007-2008 Soaring Eagle Book Award | | Nominated | |
| Maximum Ride: Saving the World and Other Extreme Sports | 2008 Buckeye Children's & Teen Book Award | | Nominated | |
| The 8th Confession (with Maxine Paetro) | 2009 Goodreads Choice Awards | Mystery & Thriller | Nominated | |
| Maximum Ride: The Final Warning | 2009 Kids' Book Choice Awards | Author of the Year | Finalist | |
| Maximum Ride: MAX | 2011 Buckeye Children's & Teen Book Award | | Nominated | |
| Now You See Her (with Michael Ledwidge) | 2011 Goodreads Choice Awards | Mystery & Thriller | Nominated | |
| Fang: A Maximum Ride Novel | 2011 Children’s Choice Book Awards | Teen Choice Book of the Year | Nominated | |
| Women's Murder Club: 11th Hour (with Maxine Paetro) | 2012 Goodreads Choice Awards | Mystery & Thriller | Nominated | |
| Guilty Wives (with David Ellis) | 2012 Goodreads Choice Awards | Mystery & Thriller | Nominated | |
| Middle School: The Worst Years of My Life (with Chris Tebbetts) | 2012-2013 Soaring Eagle Book Award | | Nominated | |
| 2012 Kids' Book Choice Awards | Author of the Year | Finalist | |
| First Love (with Emily Raymond) | 2015 Audie Awards | Romance | Nominated | |
| Cross Justice | 2017 Audie Awards | Thriller or Suspense | Won | |
| The President is Missing (with Bill Clinton) | 2018 Goodreads Choice Awards | Mystery & Thriller | Nominated | |
| All-American Murder: The Rise and Fall of Aaron Hernandez, the Superstar Whose Life Ended on Murderers' Row (with Alex Abramovich and Mike Harvkey) | 2018 Goodreads Choice Awards | Non-Fiction | Nominated | |
| Word of Mouse (with Chris Grabenstein) | 2019 Children's Literature Association of Utah Bee Hive Book Awards | Children's Fiction | Nominated | |
| Along Came a Spider: 25th Anniversary Edition | 2020 Audie Awards | Mystery | Nominated | |
| The House of Kennedy (with Cynthia Fagen) | 2020 Goodreads Choice Awards | History & Biography | Nominated | |
| Ali Cross | 2020 Goodreads Choice Awards | Middle Grade & Children's | Nominated | |
| 2023-2024 Indian Paintbrush Book Award | | Third Place | |
| Walk in My Combat Boots (with Matt Eversmann & Chris Mooney) | 2021 Goodreads Choice Awards | History & Biography | Nominated | |
| Best Nerds Forever (with Chris Grabenstein) | 2021 Goodreads Choice Awards | Middle Grade & Children's | Nominated | |
| Becoming Muhammad Ali (with Kwame Alexander) | 2022 Mangolia Book Awards | Grades 3-5 | Won | |
| 2023 Grand Canyon Reader Award | | Won | |
| 2023 South Dakota Children's Book Awards | | Won | |
| The House of Wolves (with Mike Lupica) | 2024 International Thriller Writers Awards | Audiobook | Nominated | |