He joined the Methodists at an early age and participated in preaching in Yorkshire. In 1834, Thompson emigrated to Upper Canada and settled in Toronto. On July 22, 1836, Thompson was ordained an elder in the church by John Taylor.
Thompson moved to Kirtland, Ohio, where the majority of Latter Day Saints were gathering.
Later that month, the couple traveled to Upper Canada as missionaries for the church. They returned to Kirtland in March 1838.
In 1839, the Thompsons attempted to settle in Missouri with a large number of other Latter Day Saints. He was standing next to Apostle David West. Patten when Patten was killed at the Battle of Crooked River.
In March 1839, Thompson was the clerk to the disciplinary council convened by Brigham Young that excommunicated a number of prominent Latter Day Saints and Danites, including George M. Hinkle, Sampson Avard, John Corrill, Reed Peck, West.W. Phelps, Frederick G. Williams, Thomas B. Marsh, Burr Riggs, and others
At a conference of the church in May 1839, Thompson, Almon West. Babbitt and Erastus Snow were appointed to be a traveling committee that was charged with "gather up and obtain all the libelous reports and publications which had been circulated against the Church."
On September 15, 1840, Thompson delivered the funeral oration at the funeral of Joseph Smith, Senior, the presiding patriarch of the church. In October 1840, Thompson succeeded Elias Higbee as official Church Historian, and in November of that year, Thompson and Higbee together drafted a petition to the United States Congress for redress of the grievances of the Latter Day Saints from their experiences in Missouri. Thompson was a colonel and an aide-de-camp in the Nauvoo Legion.
On May 1, 1841, he became an associate editor of the Times and Seasons newspaper in Nauvoo, Illinois.
Due to the unhealthy conditions in the offices of the Times and Seasons, Thompson and chief editor Don Carlos Smith both died from tuberculosis in August 1841.
In May 1836, he was baptized a member of the Church of the Latter Day Saints by Parley P. Pratt, a missionary who was preaching in Toronto.