Hughes joined the United States Army after the Civil War and on July 28, 1866, he was commissioned as a captain in the 18th United States Infantry. On March 2, 1867, he received a brevet promotion to major in the regular army to recognize his conduct at Fort Gregg. On July 5, 1870, Hughes was transferred to the 3rd United States Infantry. He served in several American Indian Wars, including the Great Sioux War of 1876. 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. 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. Hughes continued to serve as Terry's aide for eleven years.