* The God Delusion (2006)
* The Devil's Chaplain (2011)
* Jesus: The Unauthorized Biography (2015)
* The Reluctant Atheist: A Novel of Discovery and Recovery (2020)
Non-fiction
* Unholy Terror: The Truth Behind the Islamic State and Its Global Ambition (2016)
* We Need to Talk About God: A Neuroscientist's Guide to the Soul (2019)
* Why People Believe in God: A Neuroscientist Explores the Biology of Religious Faith (2022)
Short stories
* "The Last Miracle" (2014)
* "The Day the Angels Fell" (2015)
* "The Man Who Met God" (2016)
Essays
* "Can Science Explain Religion?" (2017)
* "The Future of Religion in a Secular Age" (2018)
* "Why I Believe in God" (2019)
Autobiography
* The Boy Who Talked to God: A Memoir (2022)