In 1830 Morgan's parents moved from Alabama to a farm near Lexington, Ky. He received a public-school education in Lexington. In 1846 he enlisted in the army and saw action at Buena Vista during the Mexican War.

In the 1850s Morgan concentrated on his prosperous hemp-manufacturing business. In September 1861 he joined the Confederate army as a scout, but by early 1862 he held the rank of captain and had a cavalry squadron under his command. He then launched lightninglike raids on Union supply lines in Kentucky and Tennessee, avoiding open combat whenever possible. Swift movement, interruption of enemy telegraphic communications, destruction of Union transportation facilities, and the dismounting of horse soldiers for combat characterized Morgan's cavalry methods. By April 1862 he had been promoted to colonel, and before the end of the year he was a brigadier general in command of a cavalry division.

Morgan began a new series of raids in spring 1863 and was authorized to raid Kentucky with 2,000 men in June and July. But Morgan went beyond his authorization and on July 8 crossed the Ohio River into Indiana. Hotly pursued by Union troops and local forces, Morgan and his men were unable to inflict much damage and suffered heavy casualties. The raid succeeded only in taking Union pressure off General Braxton Bragg's army and prolonging Confederate control of eastern Tennessee.

On July 19 most of Morgan's men surrendered, but Morgan rode on until surrounded and captured near New Lisbon, Ohio, on July 26. Four months later, he escaped from the Ohio State Penitentiary, and by spring 1864 he was back in command of a Confederate army (the Department of Southwest Virginia). He began raiding Kentucky once again and then decided to attack Union forces at Knoxville, Tenn. But on Sept. 4, 1864, he was surprised by a Federal force at Greenville and killed while trying to join his men.