A native of Canonsburg, Pennsylvania, he was educated at local academies and taught school before attending Jefferson College.

He left college to join the Union Army for the American Civil War, and rose to the rank of colonel by brevet.

He participated in engagements of the American Indian Wars, and served for several years as aide-de-camp to Alfred Terry, who became his brother-in-law.

[1] He attended Jefferson College in Canonsburg as a member of the class of 1860, but left before graduating in order to join the military during the American Civil War.

[1][2] On April 25, 1861, Hughes enlisted in the Union Army for the American Civil War, joining Company E, 12th Pennsylvania Infantry Regiment as a private.

[1] The 12th Pennsylvania was one of the many regiments created to perform three months' service at the start of the war, and Hughes served until he was mustered out with the rest of his unit on August 5, 1861.

[1] 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.

[1] During the 1876 campaign, he was assigned as aide-de-camp to his brother-in-law, Major General Alfred Terry, who commanded one of three columns of troops that fought American Indian tribes in Montana.

[1] While on Terry's staff, Hughes authored a critique of George Armstrong Custer's actions leading up to and during the Battle of the Little Bighorn.

[5] During the Spanish–American War, Hughes served in the Philippines as a member of the staff of Elwell Stephen Otis, who commanded the Eighth Army Corps.

[7] When a large fire threatened to consume the city in February 1899, Hughes led the army's response, and was officially commended by Otis.