Whitthorne was born near Farmington, Tennessee in Marshall County. He attended Campbell Academy in Lebanon, Tennessee and subsequently East Tennessee College (now the University of Tennessee) where he graduated in 1843. He subsequently studied law and was admitted to the bar in 1845, serving in various governmental positions until he entered private practice in 1848 in Columbia, Tennessee.

He served in the Tennessee State Senate from 1855 to 1858 and then as Speaker of the Tennessee House of Representatives from 1859 to 1861. In 1861 he became Adjutant General of Tennessee for the Confederacy, serving in that capacity until the end of the Civil War in 1865.

In 1870 his full civil rights were restored to him by act of Congress, and that year he began a campaign for the United States House of Representatives. He was successful, and served six consecutive terms during his initial service in the House, chairing the House Committee on Naval Affairs from 1875 to 1881.

Upon the resignation of Senator Howell E. Jackson, Whitthorne was appointed to the U.S. Senate by governor of Tennessee William B. Bate and then subsequently elected to the balance of the term by the Tennessee General Assembly, serving in the Senate from April 16, 1886 to March 3, 1887. Following his Senate service he served two more subsequent consecutive terms in the U.S. House, from 1887 to 1891. He returned to Columbia and died there later in 1891, being interred at Rose Hill Cemetery. Whitthorne Middle School in Columbia, formerly Whitthorne Junior High School, is named in his honor.