In the autumn of 1862, during the American Civil War, Faulkner raised a company of volunteers. He joined the company as a private, but was quickly promoted to captain and then lieutenant colonel of the 136th New York Infantry Regiment. When he was discharged in January 1865, he had the brevet rank of brigadier-general for gallantry. For a long time, he commanded his regiment, and at one point also commanded the brigade it was attached to. He participated in a number of important battles during the War, including Fredericksburg, Gettysburg, Chattanooga, and Resaca. He was with General Sherman during the March to the Sea.