On October 11, 1861, Hughes joined the 85th Pennsylvania Infantry Regiment and received his commission as a first lieutenant. He was promoted to captain on May 20, 1862. On December 6, 1864, he was discharged so he could join the 199th Pennsylvania Infantry Regiment. On December 7, he was commissioned as the 199th's lieutenant colonel, its second-in-command. When his commander was promoted to brigadier general and command of a brigade, Hughes ascended to command of the regiment. He served through the end of the war and was discharged on June 28, 1865. Hughes received a promotion to colonel of volunteers by brevet to recognize his gallant and distinguished service during the Union Army's April 2, 1865, assault on Fort Gregg, Virginia during the Third Battle of Petersburg.