| 2025 | Songs for Other People’s Weddings | Library Journal Best Books source ↗ (opens in a new tab) | Selection · Fiction | |
| 2023 | Answers In the Pages | Lambda Literary Awards source ↗ (opens in a new tab) | Finalist · LGBTQ+ Middle Grade | |
| 2023 | Ryan and Avery | School Library Journal Best Books of the Year source ↗ (opens in a new tab) | Selection · Young Adult | |
| 2022 | Answers in the Pages | Chicago Public Library Best of the Best source ↗ (opens in a new tab) | Selection · Best Fiction for Older Readers | |
| 2022 | Answers in the Pages | School Library Journal Best Books of the Year source ↗ (opens in a new tab) | Selection · Middle Grade | |
| 2021 | The Mysterious Disappearance of Aidan S. (as Told to His Brother) | New York Public Library Best Books source ↗ (opens in a new tab) | Selection · Best Books for Kids | |
| 2021 | Take Me with You When You Go | School Library Journal Best Books of the Year source ↗ (opens in a new tab) | Selection · Young Adult | |
| 2014 | Two Boys Kissing | Lambda Literary Awards source ↗ (opens in a new tab) | Winner · Children’s/Young Adult | |
| 2014 | Two Boys Kissing | Stonewall Book Awards source ↗ (opens in a new tab) | Honor · Children's and Young Adult | |
| 2013 | Every Day | Lambda Literary Awards source ↗ (opens in a new tab) | Finalist · Children’s/Young Adult | |
| 2013 | Two Boys Kissing | National Book Awards source ↗ (opens in a new tab) | Longlist · Young People's Literature | |
| 2013 | Every Day | Nebula Award (Novel, Novella and Andre Norton) source ↗ (opens in a new tab) | Nominee · Andre Norton | |
| 2013 | Two Boys Kissing | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Young Adult Fiction | |
| 2012 | The Lover’s Dictionary | Alex Awards source ↗ (opens in a new tab) | Winner · Adult Books for Teens | |
| 2012 | Every Day | Chicago Public Library Best of the Best source ↗ (opens in a new tab) | Selection · Best Teen Fiction | |
| 2012 | Every Day | Booklist Editors' Choice source ↗ (opens in a new tab) | Selection · Books for Youth: Fiction, Older Readers | |
| 2012 | Every Day | School Library Journal Best Books of the Year source ↗ (opens in a new tab) | Selection · Fiction | |
| 2012 | Every Day | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Teen | |
| 2012 | Every Day | Amazon Editors' Best Books of the Year source ↗ (opens in a new tab) | Selection · Top 100 | |
| 2011 | Will Grayson, Will Grayson | Stonewall Book Awards source ↗ (opens in a new tab) | Honor · Children's and Young Adult | |
| 2011 | The Lover's Dictionary | Goodreads Choice Awards source ↗ (opens in a new tab) | Nominee · Fiction | |
| 2011 | The Lover’s Dictionary | Booklist Editors' Choice source ↗ (opens in a new tab) | Selection · Adult Books for Young Adults: Fiction | |
| 2011 | The Lover's Dictionary | Amazon Editors' Best Books of the Year source ↗ (opens in a new tab) | Selection · Top 100 | |
| 2010 | Will Grayson, Will Grayson | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Teen | |
| 2009 | How They Met & Other Stories | Lambda Literary Awards source ↗ (opens in a new tab) | Finalist · Children’s/Young Adult | |
| 2007 | The Full Spectrum | Lambda Literary Awards source ↗ (opens in a new tab) | Winner · Children’s/Young Adult | |
| 2006 | Nick & Norah’s Infinite Playlist | Kirkus Best Books of the Year source ↗ (opens in a new tab) | Selection · Children's | |