Morgan received a commission in the regular Texas Army under Sam Houston as a lieutenant, and rose to captain commanding the post at Galveston.

[1] Morgan, due to his previous military experience in two wars, was appointed as a brigadier general in the Union Army on November 21, 1861, reporting to Maj. Gen. Don Carlos Buell in the Western Theater.

In March 1862, Morgan assumed command of the 7th Division of the Army of the Ohio and was ordered to southeastern Kentucky to drive the Confederates from the strategic Cumberland Gap and occupy it.

However, in September, he was forced to hastily retreat towards the Ohio River as Braxton Bragg invaded Kentucky, cutting off his supply routes.

George Morgan's 8,000 men marched over 200 miles from Cumberland Gap in sixteen days to Greenup, Kentucky, arriving there on October 3 on their way to Camp Dennison in Ohio.

Sherman, however, was upset with Morgan's performance at the battle of Chickasaw Bluffs, when he failed to carry out orders for a planned attack.

[2] Morgan soon redeemed himself as he subsequently led the XIII Corps force that captured Fort Hindman in Arkansas.

His health having deteriorated from the lengthy campaigning, and dissatisfied with the use of black troops, Morgan resigned his commission on June 8, 1863, and returned to Ohio and civilian life.

While strongly in favor of maintaining the Union at any cost, Morgan was equally opposed to any interference with slavery, believing that the Federal government had no legal right to abolish the practice.

Nonetheless, he continued to pursue a political career, and in 1866 was elected to the Fortieth United States Congress from Ohio's 13th District, serving on the Committee on Foreign Affairs.