- Meeting Jesus Again for the First Time (1994)
- The God We Never Knew: Beyond Dogmatic Religion to a More Authentic Faith (1997)
- God at 2000 (2000)
- Jesus and Buddha (2000)
- The Meaning of Jesus: Two Visions (2000)
- Reading the Bible Again For the First Time: Taking the Bible Seriously But Not Literally (2001)
- The Heart of Christianity: Rediscovering A Life of Faith (2003)
- The Last Week: A Day-by-Day Account of Jesus's Final Week in Jerusalem (with John Dominic Crossan - 2003)
- Jesus: Uncovering the Life, Teachings, and Relevance of a Religious Revolutionary (2006)
- The First Christmas: What the Gospels Really Teach About Jesus' Birth (2007)
- The First Paul: Reclaiming the Radical Visionary Behind the Church's Conservative Icon (2009)
- Putting Away Childish Things: A Tale of Modern Faith (2010)
- Speaking Christian: Why Christian Words Have Lost Their Meaning and Power and How They Can Be Restored (2011)
- Evolution of the Word: The New Testament in the Order the Books Were Written (2012)
- Convictions: How I Learned What Matters Most (2014)
- Days of Awe and Wonder: How to be a Christian in the 21st Century (2017)