Thompson, John S.. "The Jaredite Exodus: A Literary Perspective of a Historical Narrative." Journal of Book of Mormon Studies 3, no. 1 (1994): 104-112.

Thompson, John S.. "Hoyt W. Brewster Jr., Isaiah Plain and Simple: The Message of Isaiah in the Book of Mormon." FARMS Review of Books 9, no. 2 (1997): 11-15.

Thompson, John S.. "Isaiah 50-51, the Israelite Autumn Festivals, and the Covenant Speech of Jacob in 2 Nephi 6-10." In Isaiah in the Book of Mormon, edited by Donald W. Parry and John W. Welch, 123-150. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1998.

Thompson, John S., and Eric Smith. "Isaiah and the Latter-day Saints: A Bibliographic Survey." In Isaiah in the Book of Mormon, edited by Donald W. Parry and John W. Welch, 445-509. Provo, UT: Foundation for Ancient Research and Mormon Studies, 1998.

Thompson, John S.. "Lehi and Egypt." In Glimpses of Lehi's Jerusalem, edited by John W. Welch, David Rolph Seely and Jo Ann H. Seely, 259-276. Provo, UT: Foundation for Ancient Research and Mormon Studies, 2004.

Thompson, John S.. "The Lady at the Horizon: Egyptian Tree Goddess Iconography and Sacred Trees in Israelite Scripture and Temple Theology." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 38 (2020): 153-178.

Thompson, John S.. "“We May Not Understand Our Words”: The Book of Abraham and the Concept of Translation in The Pearl of Greatest Price." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 41 (2020): 1-48.

Thompson, John S.. "“Being of that Lineage”: Generational Curses and Inheritance in the Book of Abraham." Interpreter: A Journal of Latter-day Saint Faith and Scholarship 54 (2022): 97-146.

Thompson, John S., and Jackson Abhau. "Mark 1." In New Testament Minute: Mark, edited by John W. Welch. Vol. 2. Springville, UT: Scripture Central, 2023.

Thompson, John S., and Jackson Abhau. "Mark 2-5." In New Testament Minute: Mark, edited by John W. Welch. Vol. 2. Springville, UT: Scripture Central, 2023.

Thompson, John S., and Jackson Abhau. New Testament Minute: Mark In New Testament Minute, Edited by John W. Welch. Vol. 2. Springville, UT: Scripture Central, 2023.