Pvt. Warren was captured June 11, 1864 during the Battle at Trevillian Station. He was sent to Fortress Monroe, Va. on June 20th and was transferred to Point Lookout, Md. He was paroled at Point Lookout and was exchanged at Aikens Landing, Va. on September 18, 1864. On the September/October roll, he was listed as absent as a "Paroled Prisoner".
Pvt. J.J. Warren was paroled after the war at Hartwell, Ga. on May 23, 1865.