Francis Marion Lyman was born 12 January 1840 at the Justice Morse home in Walnut Grove Township (later Good Hope), McDonough County, Illinois, the son of Amasa Mason Lyman and Maria Louisa Tanner. At age eight Francis was assigned to drive an ox team in his father's pioneer company, starting west from Winter Quarters on 30 June 1848. On 1 July at the Elkhorn River he was baptized and confirmed a member of the Church of Jesus Christ of Latter-day Saints by his father. They arrived at the Great Salt Lake Valley on 19 October 1848.

Francis Lyman's family moved to San Bernardino in 1851 under assignment to establish a Mormon settlement, which they promoted until their return to Utah during the winter of 1857-58. Francis became employed in freighting and animal handling, making sixteen trips between Utah and California. In August 1856 he began courting Rhoda Taylor, an LDS immigrant from Australia; but he met resistance from her mother because he had become addicted to smoking. Eventually they married, on 18 November 1857. In late March 1858, in response to the Utah War situation and by order of Mormon Church President Brigham Young, Amasa Lyman selected Francis and seven other men to explore the Colorado River to determine whether an army could approach from that direction. They reported in May that there was no such danger.

Francis finally succeeded in breaking his smoking habit, and from then on he held the Word of Wisdom as "a great principle of liberty, an essential for strong bodies and minds, a thing indispensable to the work men are sent on earth to do." On 7 January 1860 Francis Lyman was ordained to the church priesthood office of a Seventy. In May of that year, he and his father went on missions to England. Francis married Clara Caroline Callister in 1869, and her sister Susan in 1884, firmly believing polygamy to be God's law.

Francis Lyman served as secretary and treasurer of the Fillmore and Tooele co-ops, and with his father built and operated a sawmill and the OK Flouring Mills. He became both a political and a religious leader. He served as an assistant assessor of U.S. Internal Revenue, a lieutenant-colonel in the militia at age 25, a territorial legislator, a State of Deseret General Assembly member, a county clerk and recorder, a superintendent of schools, and a prosecuting attorney. Lyman had a talent with youth, serving on the Sunday School Union Board and on the general board of the Young Men's Mutual Improvement Association. He was thorough in keeping genealogical records as well as a detailed journal throughout his life. He served as Tooele Stake President, and on 27 October 1880 he was ordained an apostle by John Taylor.

Apostle Lyman filled an Indian mission in 1882. He served as president of the European Mission from 1901 to 1904, succeeding both his father Amasa and his brother Platte in that calling. He became president of the Quorum of Twelve Apostles on 6 October 1903. Francis M. Lyman died 18 November 1916 at Salt Lake City, Utah.