He taught history and religion at BYU-Hawaii from 2000 to 2001 and joined the faculty in the Department of Church History and Doctrine at Brigham Young University in Provo, Utah, in 2002. Since that time he has also served as an editor of The Joseph Smith Papers, working on volumes in the Revelations and Translations Series and the Documents Series.[3]
Harper has also been co-editor of Prelude to the Restoration: Apostasy to the Restored Church with Fred E. Woods, Andrew H. Hedges, Patty Smith and Thomas R. Valletta. In 2010 Preserving the History of the Latter-day Saints that he co-edited with Richard E. Turley, Jr. was published. In 2012 Exploring the First Vision that he co-edited with Samuel Alonzo Dodge. In 2008 Regional Studies in Latter-day Saint Church History: The Pacific Isles that Harper co-edited with Fred E. Woods, Reid L. Neilson, Craig K. Manscill and Mary Jane Woodger was published.
—— (2004). "Delawares and Pennsylvanians After the Walking Purchase". Friends and Enemies in Penn's Woods: Indians, Colonists, and the Racial Construction of Pennsylvania. Pennsylvania State University Press. ISBN0-271-02384-8.
—— (2004). "Elizabeth Harris". New Dictionary of National Biography. Oxford University Press.
—— (2005). "On the Eve of the First Vision". In Susan Easton Black; Andrew C. Skinner (eds.). Joseph: Exploring the Life and Ministry of the Prophet. Salt Lake City: Deseret Book. ISBN1-59038-471-7.
—— (2005). "'Assemble Together at the Ohio'". In Susan Easton Black; Andrew C. Skinner (eds.). Joseph: Exploring the Life and Ministry of the Prophet. Salt Lake City, UT: Deseret Book. ISBN1-59038-471-7.
—— (2006). ""Every Man Walketh in His Own Way": Individualism, Revelation, and Authority in the Ohio Period". In Guy L. Dorius; Manscill; Craig James Ostler (eds.). Ohio and Upper Canada. Regional Studies in Latter-day Saint Church History. Provo, UT: Religious Studies Center. pp. 39–52. ISBN0-8425-2653-6.
—— (2007). "Mormon Authority and Identity in America". In Trepanier, Lee (ed.). Democracy, Pluralism, and Utah. Cedar City: Southern Utah University Press. ISBN978-0-935615-22-7.