Warner was one of the first people to enlist in the American Civil War. He was appointed major of the 3rd Infantry of Connecticut Volunteers on May 14, 1861. On July 21 of that year, he and his unit fought in the 1st Battle of Bull Run. The 3rd Infantry was mustered out on August 12, 1861. On January 15, 1862, Warner was appointed lieutenant colonel of the 13th Connecticut Infantry Regiment and sent to Louisiana. After the Union capture of New Orleans, the unit's colonel, Henry Birge, was made a brigadier general and Warner was promoted to colonel of the unit. He then fought in the Battle of Georgia Landing, the Battle of Irish Bend, and the Siege of Port Hudson. He then temporarily resigned due to ill health. After returning to service, he raised the 5th Louisiana Infantry Regiment for defending the Union-controlled New Orleans. He did this until resigning due to ill health on August 12, 1863. After the war, he bought a large plantation in Madison County, Mississippi, where he employed freedmen and gave them monetary wages.