At the outbreak of the war, Taylor resigned from the Louisiana state senate to become the colonel of the 9th Louisiana Infantry. He first served at the Battle of First Manassas. In October 1861, he was promoted to brigadier general. Taylor served in the Valley campaign of 1862 and in the Battle of the Seven Days' before he was promoted to major general. He was assigned to the District of West Louisiana and served in the repulse of the Red River expedition in the spring of 1864 before Taylor requested to be relieved of command. Instead, in April 1864, he was promoted to lieutenant general, as assigned to the Department of Alabama and Mississippi. In May 1865, Taylor surrendered his command.
