The Thirteenth Texas Infantry, originally called the Fourth Texas Volunteer Regiment before formal acceptance by the Confederate States of America, was mustered into service between September 17, 1861, and January 4, 1862. The initial twelve companies of the regiment were from all over the state, including the counties of Brazos, Jasper, Hopkins, Smith, and Van Zandt, and the cities of Austin, Corsicana, Columbus, and Starrville. The first commanding officer of the Thirteenth was Col. Joseph Bates, and his field officers were Lt. Col. Reuben R. Brown, Lt. Col. Henry P. Cayce, Maj. Robert L. Foard, Maj. Stephen S. Perry and Maj. Lee C. Rountree.
The unit was technically considered a legion as it was originally composed of between ten and twelve infantry, cavalry, and artillery companies, The regiment experienced considerable losses of personnel by transfer to other units throughout its existence. In April of 1862, four infantry units were transferred to the Fifteenth Texas Infantry and four others (three cavalry and one artillery) to the newly-formed Twelfth Texas Cavalry Battalion under the command of Lieutenant Colonel Brown. In the fall of 1863 Brown's Twelfth was consolidated with Major Rountree's battalion to form the Thirty-fifth (Brown's) Texas Cavalry, requiring four more companies (three cavalry and one artillery) from the Thirteenth.
The Thirteenth spent nearly the entire war on the Texas coast between Matagorda and Galveston, thus it saw only a few military engagements, most of which involved artillery exchanges with the Federal navy. The first such action occurred at San Luis Pass on April 5–6, 1862, when Union forces destroyed the schooner Columbia and its cargo of cotton and captured eight Confederate soldiers. Two more brief encounters involving shelling by Federal ships in July and August of that year led Colonel Bates to request more artillery pieces in order to protect against what he called "our defenseless condition."
In 1863 artillery detachments from the Thirteenth saw action at Galveston and Sabine Pass, and the regiment was involved in the battle at Matagorda Peninsula. On December 31, 1863, the unit lost twenty-two men when a small boat capsized in a storm during an attack on U.S. gunboats.
Poor troop morale and discipline were habitual problems for state units serving along the Texas coast for extended periods of time. This was due to the lack of military action, monotony of garrison duty, poor provisions, lack of pay, and exposure to disease in the region. The Thirteenth was included in the surrender of the Confederate Trans-Mississippi forces at Galveston in June of 1865, but most of the unit's companies had disbanded during the Texas "break up," when Confederate soldiers throughout the state realized the war was over and simply left for home.