* _Easy Travel to Other Planets_ (2003)
* _Mink River_ (2010)
* _Chicago_ (2014)
* _The Plover_ (2017)
Nonfiction
* _Angels & Fugitives_ (1994)
* _The Wet Engine & Other Stories_ (1997)
* _Holy Toledo_ (2010)
* _The Grail: A Year of Reading Together from Giraldus to Garrigou-Lagrange_ (2011, with James Matthew Wilson)
* _Tumble & Fall_ (2013)
* _The Kind of Brave: A Memoir of Courage_ (2014)
* _One Great Mystery: God's Action in the History of the World_ (2015)
* _Liturgical Year: The Spiritually Transformative Journey_ (2017, with James Matthew Wilson)
* _Grace Notes_ (2018)
* _One Long River of Song_ (2019)
Children's books
* _The Bear in My Family: A Dad & Daughter Story_ (2003)
* _St. George and the Dragon_ (2009)
Collections
* _Thirsty for God: Learning to Pray as a Child of God_ (2009)
* _The Book of Uncommon Prayer: A Novella and Stories_ (2010)
* _The Portable Brian Doyle: Collected Essays_ (2012)
* _The Grail: Ten Ways of Thinking, Drinking, and Praying_ (2014, with James Matthew Wilson)
* _On the Shores of the Narrow Sea: Collected Essays_ (2015)
* _The Church of Doubt_ (2016)
Posthumous collections
* _Peace: A Contemplative Reflection on the Gift of Gratitude_ (2019)
* _The World Is Bigger Here_ (2019)
* _Joyful Noise_ (2021)