John A. Morgan enlisted in Co. E, 7th (Desha's) Battalion Arkansas Infantry, at Pocahontas, Arkansas, on November 16, 1861. On May 7, 1862, Cos. A & E of Desha's Battalion were consolidated as (new) Co. K, 8th Arkansas Infantry. John A. Morgan was captured at Harrodsburg, Kentucky, on October 9, 1862, and exchanged at Vicksburg, Mississippi, in December. He was wounded and sent to a hospital near Atlanta, Georgia, on June 22, 1864, and took the oath of allegiance there on May 9, 1865. His original company was recruited in White County.

John A. Morgan applied for a Confederate pension from White County in 1901 (Pension #14112). He is listed in the 1911 special census of Confederate veterans, at Searcy.