After his resignation from the U.S. Army, April 1, 1861, he was appointed a brigadier general in the South Carolina Militia[1] but did not serve in that office.
[2] He was a staff officer in the Confederate States Army in the Eastern Theater of the American Civil War from April 1861 until May 31, 1862.
After Johnston was wounded on May 31, 1862, and was succeeded in command by General Robert E. Lee, Rhett was transferred to the District of Arkansas in Confederacy's Trans-Mississippi Department where he served as chief of ordnance.
[2][3][5] Rhett was appointed brevet second lieutenant in the Ordnance Department of the U.S. Army on July 1, 1845, and served at the Washington Arsenal.
[2][3][6][9] Rhett was a member of the Aztec Club of 1847, which was founded as a military society of officers who served with the United States Army in the Mexican-American War.
[5] Then he served in the Regiment of Mounted Riflemen on the frontier at posts including Fort Laramie, Dakota Territory (Wyoming), 1849–1852 and Corpus Christi, Texas, 1852–1855.
[5] On February 16, 1861, Brigadier General and Brevet Major General David E. Twiggs, a Georgia native, surrendered all U.S. forts in Texas to Texas Confederates led by Ben McCulloch, despite having been relieved of command of the Department of Texas by United States Secretary of War Joseph Holt in an order dated January 18, 1861, the day that Holt assumed office from John B. Floyd of Virginia who became a Confederate States Army brigadier general.
[2][12] From July 20, 1861, to March 14, 1862, his official position was Chief of Staff and Assistant Adjutant General in the Confederate Army of the Potomac.
[2][6][15] From May 1862 to April 1863, Rhett was chief of ordnance in the District of Arkansas, Trans-Mississippi Department of the Confederacy, serving under Lieutenant General Theophilus H. Holmes starting October 22, 1862.
[2][3][12] From April 30, 1863, to the end of the war in June 1865, Rhett was chief of artillery in the Trans-Mississippi Department, under the command of General E. Kirby Smith.