- This Our Exile: A Spiritual Journey with the Refugees of East Africa (1999)
- Becoming Who You Are: Insights on the True Self from Thomas Merton and Other Saints (2006)
- Between Heaven and Mirth: Why Joy, Humor, and Laughter Are at the Heart of the Spiritual Life (2011)
- The Jesuit Guide to (Almost) Everything: A Spirituality for Real Life (2012)
- Jesus: A Pilgrimage (2014)
- Seven Last Words: An Invitation to a Deeper Friendship with Jesus (2016)
- James Martin: Essential Writings, selected and with an introduction by James T. Keane (2017)
- Building a Bridge: How the Catholic Church and the LGBT Community Can Enter into a Relationship of Respect, Compassion, and Sensitivity (2017)