Francis Thomas Anderson Junkin was born in 1864 in Rockbridge County, Virginia, son of Anna Aylett Anderson Junkin (1833-1911) and the Rev. William Finney Junkin (1831-1900), a Presbyterian minister. He was the grandson of the Rev. George Junkin (1790-1868), founder and President of Lafayette College in Easton, Pennsylvania, and a President of Washington College (later Washington and Lee University) in Lexington, Virginia. His aunt, Rev. William Finney Junkin's sister, Elinor (1825-1854), was the first wife of Thomas "Stonewall" Jackson (1824-1863).

Junkin attended Kenyon College and Columbia University, where he received a law degree in 1887. He practiced law in New York City until 1898. He was appointed General Attorney of the Atchison, Topeka & Santa Fe Railroad in 1899. He resided in Chicago and New York City, but retained close ties with Lexington and Rockbridge County. His sister, Elinor Jackson Junkin Cox Latane (1867-1939), purchased "Mulberry Hill" in 1903 where she lived with their mother. The property was originally built by Junkin's ancestors and changed hands a number of times in the 19th century. The house still stands on the outskirts of Lexington.

Junkin first showed interest in genealogy in 1878 when he wrote to his mother's cousin, William Winston Fontaine (1834-1917), seeking information about the family. By the early 20th century he was corresponding regularly and at length with relatives regarding family history. He completed a large genealogy chart in 1908, and continued pursuing personal information on the families represented on the chart as well as more distant connections. He married Emily Hutchison Crane (ca. 1866-n.d.) in Paris, France in 1913. On 15 September 1919 Junkin was appointed a member of the Board of Contract Adjustment with the rank of Lieutenant Colonel in the Army. The board was created as a court of final appeals in adjusting claims against the U.S. Government arising after the end of World War I. Junkin lived in Washington, D.C. from 1920 until his death on 6 May 1928.

Francis T.A. Junkin also had connections to the Rust family in Loudoun County, Virginia. His niece, Lily Lawrence Rust Fendall (1880-1973), was the granddaughter of Armistead Thomson Mason Rust (1820-1887) of "Rockland" Leesburg, Virginia and his first wife, Eliza Southgate Lawrence (1828-1958). Junkin's sister, Elinor, was first married to Lewis Berkeley Cox (1856-1901) of "Stoke" in Aldie, Virginia. Their son, William Junkin Cox (1896-1989), was married twice, first to Ida Lee Edwards (1898-1950) and second to Jane Rust (1918-1977). Both women were granddaughters of Armistead Rust and his second wife, Ida Lee (1840-1921). William Junkin Cox's descendants still live in Leesburg.