| 2017 | The Asylum of Dr. Caligari | Shirley Jackson Awards source ↗ (opens in a new tab) | Nominee · Novella | |
| 2016 | Galápagos Regained | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2016 | Reality by Other Means: The Best Short Fiction of James Morrow | World Fantasy Award (Novel, Collection and Anthology) source ↗ (opens in a new tab) | Nominee · Collection | |
| 2010 | Shambling Towards Hiroshima | Hugo Award (book categories) source ↗ (opens in a new tab) | Finalist · Novella | |
| 2010 | Shambling Towards Hiroshima | Nebula Award (Novel, Novella and Andre Norton) source ↗ (opens in a new tab) | Nominee · Novella | |
| 2009 | The Philosopher's Apprentice | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2007 | The Last Witchfinder | John W. Campbell Memorial Award for Best Science Fiction Novel source ↗ (opens in a new tab) | Finalist · Best Science Fiction Novel | |
| 2007 | The Last Witchfinder | Locus Awards source ↗ (opens in a new tab) | Finalist · Fantasy Novel | |
| 2006 | The Last Witchfinder | Otherwise Award source ↗ (opens in a new tab) | Honor · Otherwise Award | |
| 2006 | The Last Witchfinder | BSFA Awards source ↗ (opens in a new tab) | Shortlist · Best Novel | |
| 2006 | The Last Witchfinder | Washington Post Best Books of the Year source ↗ (opens in a new tab) | Selection · Notable Fiction | |