Paul Jones was laid down on 20 April 1899, by the Union Iron Works of San Francisco; launched on 14 June 1902; sponsored by Mrs. Elizabeth Goldsborough Adams; and commissioned on 19 July 1902.

Originally built as a torpedo boat destroyer, Paul Jones served in the Pacific Fleet, homeported at San Francisco.

She then commenced training operations, in conjunction with other duties, off Norfolk, Lynnhaven Roads, and Chesapeake Bay, prior to reporting to Philadelphia on 20 December.

Wallowing in stormy seas with her after fire room flooded, barely able to maintain headway, having lost all drinking and feed water and steaming under two boilers with salt feed, manning bucket brigades for lack of operable pumps, and receiving no answers to her distress signals, she finally sighted a light off St. David's Head, Bermuda, signalled the fort for assistance and dropped her anchor.

Following permanent repairs at the Philadelphia Navy Yard, Paul Jones reported to Fortress Monroe, Virginia on 18 April, and performed various duties in and around the Chesapeake Bay until 6 August.

Paul Jones reported at Hampton Roads, Virginia, on 9 August 1918 and remained in and around the Chesapeake Bay conducting mine patrols, convoy duties, and other services until slated for inactivation on 31 January 1919.

She decommissioned on 29 July; was struck from the Naval Vessel Register on 15 September; and was sold on 3 January 1920 to Henry A. Hitner's Sons Company, Philadelphia, who subsequently scrapped her.