John Doyle Lee was born on 12 September 1812 in Kaskaskia, Illinois Territory, about one hundred miles south of St. Louis. After the successful American Revolution, John Doyle, Lee's maternal grandfather, had traveled to Illinois from Virginia to claim 400 acres of frontier land allotted under the grant of 1787, earned as part of his military service. Lee's mother was Doyle's first daughter, Elizabeth. She married Ralph Lee, on 26 February 1811.

Ralph Lee was related to the Lees of Virginia and plied the carpenter's trade. When Elizabeth's health failed, Ralph began drinking to excess. In May 181 they executed a deed of trust to care for their children. Elizabeth died in November 1815. John D. spent the next four years in the care of a black nurse, in the home of John Doyle, who died in 1819. At that time John D. went to live with his uncle, James Conner, and his wife, Charlotte. They had six children, and John D. soon felt like an extra child where there were already too many.

At age twenty, John D. left to find work. He worked on a steamboat and proved his trustworthiness to a merchant, a Mr. Boggs, at Galena, Illinois, where he learned more of the world and business. When he moved to Vandalia, where his sister Elizabeth lived, he became acquainted with Aggatha Ann Woolsey, whom he married 24 July 1833 after a brief courtship.

Introduced to the LDS Church, Lee and his wife moved to Far West, Missouri, in June 1838 and began the association which influenced the rest of his life. Lee and his wife were baptized on 17 June 1838 after meeting Joseph Smith for the first time. The experience of baptism was powerful enough to cause him to dedicate his life to the Mormon Church. As part of the work of building up the Kingdom of God, Lee eventually married eighteen more women and fathered sixty children. Lee became a member of the Danites, a secret fraternal order that was pledged to defend the rights of Mormons. Election day, 6 August 1838, provided Lee an opportunity to defend the rights of Mormon voters when Missourians who objected to Mormons voting started a riot. When one member of the secret order made the sign of distress, eight others, including Lee, waded in with clubs and brought calm to the street. Organized marauders on both sides set loose looting and burning; Lee later admitted to looting. Governor Lilburn Boggs sent in the state militia with his "Extermination Order" to protect the public good. The Mormons, including Lee, left Missouri for Nauvoo, Illinois.

Lee served several brief missions in nearby states and enjoyed success as a preacher, organizer, and healer. He returned to Nauvoo in August 1843 and resumed his duties as a guard at the home of Joseph Smith--a duty he regarded as a privilege. He felt that, "save Jesus Christ," no greater man than the Mormon Prophet had ever lived. When spring came, Lee was called on another mission and went to eastern Kentucky, where he was serving in June 1844 when Joseph and Hyrum Smith were murdered. He returned in August to face a new and threatening situation from neighbors who did not want Mormons in Illinois. Brigham Young, the de facto leader of the Mormons, had started preparations for a move to the West where the Mormons could practice their religion in peace.

Lee was a member of the "Council of Fifty," an organization of Mormon leaders. Lee's role proved to be as a clerk and purchasing agent, positions in which his skills proved valuable. When the first party of pioneers left for the Great Basin in 1847, Lee and his family stayed in Iowa, sixteen miles north of Winter Quarters at "Summer Quarters," to farm and raise crops for those left behind and others to follow. On his own journey across the plains the next year, he was appointed a "Captain of Fifty" and secretary of the train by Brigham Young.

Once he arrived in the Great Basin, Lee, as a member of the Council of Fifty, was kept busy. Other Mormon leaders valued his industry and loyalty. In 1850 he was called to help open the Iron Mission. He took two of his wives and left the Salt Lake Valley in late December 1850. The journey was made in deep snow to what is now Parowan, Iron County. Lee returned to Salt Lake in July 1851 to move his family south to the place he planned to call his home, a place called Harmony.

In January 1856 Lee was appointed U.S. government Indian Agent in the Iron County environs. His job was to distribute tools, seed, and supplies, and to assist the Indians with farming methods. Because of this assignment, Lee became the central figure in the tragic Mountain Meadows Massacre which occurred in September 1857.

After a group of 120 to 150 California-bound men, women, and children, known as the Fancher Party, was attacked by Indians in a four-day siege while they were camped at Mountain Meadows, Lee and William Bateman met with members of the wagon train and arranged for them to be escorted to safety under a flag of truce by the Mormon militia. With no other alternative, the company surrendered their weapons, but as they marched away from their wagons, Mormon militiamen, including Lee, shot and killed the male members of the party while Indians killed the women and older children. Seventeen small children were spared and cared for by Mormon families until they were returned to relatives in Arkansas.

The reasons for the massacre are complex, but center around a wartime hysteria that had built up in Utah with the announcement in July 1857 that a federal army was en route to Utah to put down an alleged Mormon rebellion. Rumors also circulated that members of the Fancher party had stolen from the Mormons, poisoned their reservoirs, and boasted of their role in the assassination of Joseph Smith.

After the massacre, John D. Lee remained an active leader in Mormon affairs in southern Utah. However, by the late 1860s, questions about the massacre became more and more difficult to avoid, and in October 1870 Brigham Young excommunicated Lee from the Mormon Church for his role in the affair. Lee was the only one so punished and would later maintain that he became a scapegoat to take the public pressure off the more responsible Mormon leaders.

In a search for safety from arrest, in 1872 Lee moved to a remote crossing of the Colorado River, where he established Lee's Ferry, a vital link connecting southern Utah with Mormon settlements in northeastern Arizona.

Lee was arrested in November 1874, and was tried and convicted of murder at Mountain Meadows. He was taken to the massacre site, where he was executed by a firing squad on 23 March 1877. His body was buried in the Panguitch cemetery. On 20 April 1961 Lee was restored to membership in the Mormon Church.