Following shakedown in the Gulf of Mexico, Hughes joined the Atlantic Fleet. From July 1940 through December 1941, Hughes served in the Atlantic, first on patrol off Martinique to watch Vichy-controlled French Forces there and then on Neutrality Patrol off Iceland. During this time, she became the first American destroyer to escort a British convoy all the way to England.
Following the attack on Pearl Harbor, warships were urgently needed in the Pacific and Hughes sailed from Norfolk on 18 December 1941, arriving at San Diego in company with Yorktown (CV 5) on 30 December. She departed San Diego on 12 January 1942 as an escort for ships bringing reinforcements to Samoa. Hughes then sailed from Samoa as part of a carrier striking force built around Yorktown. She screened the carrier in strikes on Jaluit, Makin, Mili and the Canton Islands, and then screened the combined Lexington–Yorktoum Task Force 17 as it attacked Japanese bases at Lae and Salamaua on 10 March 1942. Missing the Battle of the Coral Sea while escorting a tanker carrying fuel to Nouméa, Hughes reached Pearl Harbor in time to participate in the Battle of Midway.
While screening Yorktown during this action, Hughes shot down two torpedo planes and assisted in shooting down two others. After Yorktown was hit on 4 June, Hughes continued an all-night vigil to prevent her capture. When the carrier was torpedoed by a submarine on 6 June, Hughes helped damage the attacker with depth charges, and then rescued survivors when Yorktown sank the next day.
After a brief time as convoy escort, Hughes joined American Forces at Guadalcanal, where she screened the carrier Hornet (CV8) throughout the campaign. During the Battle of Santa Cruz, Hughes splashed one Japanese plane and assisted in downing two more. Despite her valiant efforts, Hornet was hit and sunk on 27 October 1942. Joining Task Force 16 on 10 November 1942, Hughes participated in the Naval Battle of Guadalcanal by screening Enterprise (CV 6). Hughes continued screening operations until the end of February 1943.
Following a refit and brief convoy duty, Hughes was detached from the South Pacific and sailed to Pearl Harbor, departing on 18 April for the Aleutian Islands and arriving on the 24th. Bombardments of Kiska on 6 and 22 July were high points of her months in northern waters. After Kiska was occupied, Hughes departed the Aleutians on 25 August for overhaul in San Francisco.
Following overhaul, Hughes sailed for Pearl Harbor on 26 October to prepare for the invasion of the Gilbert Islands. She sailed on 10 November as part of the screen for the escort carriers covering the invasion of Makin Atoll. When Liscombe Bay (CVE 56) was sunk 24 November, Hughes rescued 152 of the survivors. She began screening the transport group on 27 November. Two days later, she departed for Pearl Harbor, and arrived there on 7 December 1943. On 13 January 1944, Hughes joined Task Force 53 for the invasion of the Marshall Islands. She joined in the preinvasion, 3 to 11 February 1944. The destroyer continued to support the escort carriers during the strikes against the Palaus on 31 March.
Hughes took part in the invasion of Hollandia, New Guinea on 23 April, acting as a screen for the CVE group which provided air cover for the landings at Aitape and Tanahmerah Bay. Then Hughes remained off New Guinea as a convoy escort and fire-support ship of the Seventh Fleet until 25 September, when she departed for the invasion of the Philippines. During this time, Hughes participated in the invasions of Biak, Noemfoor, Cape Sensapor and Morotai, serving as flagship of Rear Adm. William M. Fechteler during the latter campaign.
During the invasion of Leyte, Hughes was the flagship of Rear Adm. Arthur D. Struble commanding the tiny task group detailed to capture the small islands of Dinagat and Homonhon guarding the entrance to Leyte Gulf. Following the successful conclusion of this operation, Hughes screened Philippine-bound convoys, making frequent trips to and from New Guinea until 6 December 1944, when she reembarked Admiral Struble and departed for the invasion of Ormoc Bay, Leyte. Following this operation, on 10 December 1944, Hughes was serving as a picket destroyer off the southern tip of Leyte when she was hit by a kamikaze. Badly damaged with one engine room demolished and much of her other machinery destroyed, Hughes was towed to San Pedro Bay, Leyte, where, after temporary repairs, she departed for Humboldt Bay, New Guinea on 19 December en route to Pearl Harbor, where she arrived 23 on January 1945. Following more repairs, she sailed for San Francisco, arriving at Hunter’s Point Naval Drydocks on 2 February. Hughes remained there for the next three months undergoing extensive overhaul.
After a long testing period, Hughes was declared combat ready and departed for Adak in the Aleutians on 4 June 1945. Assigned to the Northern Pacific Force, she remained in the Aleutians until the end of the war, harassing enemy shipping and bombarding Japanese bases. Hughes then served as part of the patrol force off Northern Honshu until relieved on 20 October. She sailed for the United States 10 days later with Destroyer Squadron 2. She was decommissioned on 28 August 1946 and struck from the Navy List 26 on November 1948.
Hughes earned 14 battle stars for World War II service.
