James Fleming Fagan was born in Louisville, Clark County, Kentucky on 1 March 1828. Fagan's family moved to Little Rock, Arkansas when his father was hired to work on the Old State House. His father died during his youth and his mother, Catherine A. Fagan, married Samuel Adams in 1842 who became Governor of Arkansas in 1844.
After his stepfather's death James Fagan took control of the family farm along the Saline River in southern Arkansas. Though he was a member of the Whig Party he represented the heavily Democratic Saline County in the Arkansas legislature.
Fagan served in the United States Army during the Mexican War in the Arkansas regiment under General Archibald Yell and was promoted to the rank of Lieutenant during the war.
At the start of the Civil War Fagan raised a company for the Confederate States Army and became its Captain. When his unit was folded in with 1st Arkansas Infantry Regiment Fagan was elected as Colonel of the regiment.
Fagan was promoted to Brigadier General on 12 September 1862 and commanded a brigade composed of Arkansas regiments. Fagan played a central role in the Battle of Helena where he and his brigade made repeated assaults on Federal artillery batteries.
Fagan participated in the Arkansas portion of the Red River Campaign and played a central role in the battles during that campaign including the successful destruction of a Federal supply train at the Battle of Marks' Mill which led to the Federal retreat from southern Arkansas.
Fagan was promoted to Major General on 24 April 1864 and commanded the Arkansas division of Confederate cavalry during Price's Raid into Missouri.
The end of the war found him in command of the District of Arkansas of the Trans-Mississippi Department and was active militarily until late April of 1865.
General Fagan's first wife was the sister of General William Nathan Rector Beall. Fagan was also related by marriage to Governor Henry Massey Rector.
Fagan was not paroled by the US government until 20 June 1865. After his parole he returned to his farm to make a living. He was appointed United States Marshal by President Ulysses S. Grant in 1875. He served as a receiver for the United States Land Office in 1877. In 1890 he ran for Arkansas Railroad Commissioner but was defeated.
James Fleming Fagan died in Little Rock, Arkansas on 1 September 1893. Fagan is buried at the historic Mount Holly Cemetery in Little Rock.