A lawyer and Mexican War veteran, James Archer resigned his captain's commission in the regular army on March 14, 1861, to receive the same rank in the Confederate service two days later. Although a Marylander, Archer was appointed colonel, 5th Texas, a regiment organized in Richmond from independent companies, on October 2,1861. He commanded his regiment, and sometimes the brigade, at the batteries at Evansport along the Potomac and on the Peninsula in the actions at Eltham's Landing and Seven Pines. He was promoted brigadier general, CSA, June 3, 1862, and given command of Hatton's old brigade of Alabama, Georgia, and Tennessee troops (that officer having been killed at Seven Pines). The Georgians were eventually transferred out and replaced by more Alabamians, but the brigade became known as the Tennessee Brigade. Archer's commands in the Army of Northern Virginia included: Tennessee Brigade, A. P. Hill's Division June 3-July 1862); Tennessee Brigade, A. P. Hill's Division, Jackson's Corps (July 27, 1862-May 30, 1863); Tennessee Brigade, Heth's Division, A. P. Hill's Corps (May 30-July 1, 1863); and Archer's and Walker's Brigades, Heth's Division, A. P. Hill's Corps (August 19-October 24, 1864).

Commanding his brigade, Archer took part in actions at Beaver Dam Creek, Gaines' Mill, Frayser's Farm, Cedar Mountain, 2nd Bull Run, the capture of Harpers Ferry, Antietam, Fredericksburg, and Chancellorsville.

On the first day at Gettysburg he was picked up by an Irishman from the Union's Iron Brigade, becoming the first general captured from the Army of Northern Virginia since Lee took command.

While imprisoned at Johnson's Island, Ohio, Archer let the Confederate War Department know through a paroled prisoner that the guards could be overwhelmed but the Southerners would have no way of getting off the island. On June 21, 1864, Archer was ordered sent to Charleston Harbor to be placed under Confederate fire in retaliation for southern treatment of prisoners. Later exchanged, Archer was ordered to the Army of Tennessee for duty on August 9, 1864, but he was redirected to the Army of Northern Virginia 10 days later.

He was assigned command of his own as well as Walker's Brigades, which had been temporarily consolidated. Suffering from the effects of his imprisonment and the rigors of the Petersburg trenches, including the battle of Peebles' Farm, Archer died on October 24, 1864.