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Jackson was born in Paris, Tennessee, a son of Dr. Alexander Jackson and Mary (Hurt) Jackson, the daughter of a Baptist minister, both natives of Virginia. At the age of five, his family moved to Jackson, Tennessee, where his father would be elected as a Whig to the state legislature and subsequently as Jackson's mayor. His brother Howell Edmunds Jackson would become a United States Supreme Court Justice.
He attended West Tennessee College (now Union University) before accepting an appointment to the United States Military Academy. He graduated from West Point in 1856 and was brevetted as a second lieutenant in the U.S. Army. He studied at the cavalry school at Carlisle Barracks and joined the Regiment of Mounted Rifles . He served on frontier duty at Fort Bliss in Texas in 1857, and engaged in a skirmish with Kiowas near Fort Craig in New Mexico Territory. He participated in the Comanche and Kiowa Expedition of 1860.
When word came of Tennessee's secession, Jackson resigned from the Army on May 16, 1861, and returned to the South to enroll in the Confederate army as a captain of artillery. He was an aide-de-camp to General Gideon Pillow and served at the Battle of Belmont in November. In early 1862, Jackson was appointed as colonel of the 1st Tennessee Cavalry and rose to be chief of cavalry under John C. Pemberton, Earl Van Dorn, and then Sterling Price. On December 29, 1862, he was promoted to brigadier general.
He served with distinction in the Vicksburg Campaign in early 1863. In February 1864, he commanded the cavalry of Leonidas Polk in the campaign around Meridian, Mississippi. During the Atlanta Campaign that summer, Jackson commanded the cavalry division of the Army of Mississippi. His troopers repeatedly skirmished in August with the Union cavalry of H. Judson Kilpatrick, which was attempting to destroy railroads south of the city. Jackson won a significant victory at the Battle of Brown's Mill near Newnan, Georgia.
He continued to lead his division through the Nashville and Murfreesboro campaign and then retreated to Mississippi. In February 1865, he was assigned command of all cavalry from Tennessee in the force of Nathan Bedford Forrest. He successfully isolated the Union brigade of John T. Croxton during Wilson's Raid in April.
Following the war, Jackson returned to Tennessee and managed his father's cotton plantation. In 1868, he married Selene Harding, and co-managed his father-in-law's estate, "Belle Meade". In the 1870s, Jackson became heavily involved in The Grange movement. He also belonged to the Tennessee Agricultural and Mechanical Association, and sat on the Tennessee Bureau of Agriculture.
In 1886, Jackson and his older brother, jurist Howell Edmunds Jackson, took over control of Belle Meade following their father-in-law William Giles Harding's death. They raised prize race horses. General Jackson purchased a stallion named Iroquois in 1886, the first American winner of the Epsom Derby.
William H. Jackson died at Belle Meade in 1903 and was buried in the family's mausoleum in the plantation's cemetery. In 1906, after the plantation was sold, he and other members of the Harding-Jackson family were reinterred in Mount Olivet Cemetery in Nashville, Tennessee.