After commissioning, Stewart served for a short time at the Naval Academy and then joined the Coast Squadron of the North Atlantic Fleet. In 1906, she was placed in reserve at Norfolk, Virginia but was recommissioned in 1907 in the Atlantic Fleet and transferred in 1908 to the Pacific Fleet. As one of the first group of destroyers built in the United States, Stewart quickly became obsolescent; and, on 24 February 1916, the Navy Department decided that destroyers numbered 1 through 16 were “no longer serviceable for duty with the fleet.” These ships were henceforth classed as “coast torpedo vessels,” but this did not prevent Stewart from having an active career in World War I.
After the United States declared war on Germany on 6 April 1917, Stewart patrolled first off the Atlantic entrance to the Panama Canal and along the Colombian coast; and then, after 11 May, off the Pacific entrance to the canal. On 5 July, she returned to the Atlantic and between 22 July and 11 August was fitted out at the Philadelphia Navy Yard for distant service.
On 13 August, Stewart sailed for Bermuda with a destroyer flotilla but, on arrival on 16 August, she grounded in the harbor. Under repair there and at Philadelphia through 10 October, she began dispatch and escort duty from a base in the York River on the 11th. Except for one interruption for training, this duty continued until 31 December 1917, when she entered the Philadelphia Navy Yard to fit out again for distant service.
Departing Philadelphia on 15 January 1918, Stewart sailed the next day for Europe with four other destroyers. Stopping at the Azores from 29 January to 4 February, Stewart and Worden arrived at Brest, France, on the 9th and began convoy escort duty off that port on the 17th.
On 17 April 1918, as Stewart entered Quiberon Bay, an American steamer, Florence H., with a cargo of powder and steel, exploded in the anchorage. Stewart saved nine survivors and her crew was cited by the Secretary of the Navy for gallantry during the rescue.
On 23 April, Stewart sighted two seaplanes dropping bombs, apparently on a submarine, and raced to the spot. One aircraft flew over the destroyer, and the observer pointed to the location of the sub. Stewart saw first the sub’s wake, then its periscope and finally the dark form of its hull underwater. She was forced to turn away at the last moment due to the effort of a French escort to ram the sub, but dropped two depth charges which brought up large amounts of oil. The action was evaluated at the time as a kill; but the submarine, U-108, survived to be damaged by Porter several days later and finally to surrender at Harwich at the end of the war.
During a dense fog three days later, Stewart was damaged when she collided with an unidentified merchantman. She remained uinder repair until 28 May.
On 4 August, the destroyer made another attack on an apparent submarine wake, but obtained no evidence of success.
After the Armistice ending World War I was signed on 11 November 1918, Stewart ceased convoy duty; and she entered drydock at Brest on 26 November for repairs. On 9 December, she departed Brest with four other destroyers and, after passing the convoy carrying President Wilson to Europe two days later and subsequently making stops at the Azores and Bermuda, arrived at Philadelphia on 3 January 1919. Decommissioned on 9 July, Stewart was struck from the Navy list on 15 September and sold on 3 January 1920 to Joseph G. Hintner Co., Philadelphia, for scrap.