J. J. Thompson was born around 1835. By the early 1860s, he was probably living in Texas.
He enlisted in the Confederate army on October 9, 1861, and he mustered in as a private in the 9th Texas Infantry. The regiment took part in the Battle of Shiloh, the Battle of Perryville, and the Battle of Stones River. He was slightly wounded at Shiloh, but he recovered and rejoined the regiment. He eventually earned a promotion to commissary sergeant. Union forces captured him on May 4, 1865, as part of General Richard Taylor’s command. He received a parole on May 11, 1865. He died sometime after the war.