Congress was built by naval constructor, James Hackett, at Portsmouth, New Hampshire. Her construction, interrupted upon conclusion of peace terms (Treaty with Algeria (1795)) with Algiers, was resumed with the imminence of naval war with France, and she was launched 15 August 1799 under the command of Captain James Sever. Congress was one of the six original frigates authorized for construction by the Naval Act of 1794.
After outfitting at Portsmouth and Boston, Congress proceeded to Newport, Rhode Island, in December 1799, then to sea to protect commerce from French despoilment. She started her maiden voyage, on 6 January 1800, in company with frigate Essex, escorting merchant ships to the East Indies, however, she lost her mast when only six days out and returned to the States. Following repairs at Hampton Roads she again sailed for the West Indies on 26 July.
On 29 August, she recaptured the merchant brig Experiment, seized three days previously by a French privateer. Sailing on the Santo Domingo station until the following year, Congress returned to Boston in April 1801 and was thereafter placed in ordinary at Washington, D.C.
The continuing piracies of the Barbary States occasioned Congress's return to commission in April 1804. Under Captain John Rodgers, she departed for Hampton Roads to join the ships of the Mediterranean Squadron, Commodore Samuel Barron. Arriving at Gibraltar on 11 August, Congress cruised vigilantly in the Mediterranean for 11 months. Now commanded by Stephen Decatur, she returned to the United States in November, carrying the Tunisian ambassador to the United States. She again laid up in ordinary at Washington until 1811.
A period of extensive repair preceded recommissioning of Congress in the fall of 1811 under the command of Captain John Smith. Early in 1812, before the War of 1812 broke out, she made several brief cruises along the eastern coast. Congress was assigned to the squadron of Commodore Rodgers, patrolling the North Atlantic, from June to August 1812. She made her second cruise against the enemy in company with the frigate President, sailing from Boston, on 8 October, and capturing nine prizes before returning on 31 December. On 30 April 1813, Congress again put to sea, cruising off the Cape Verde Islands and the Brazil coast where she captured four small enemy ships. On 14 December, she returned to Portsmouth for repairs, remaining there for the duration.
From October 1822 to April 1823, Congress, under Captain James Biddle, operated against the West Indies pirates. During the second half of 1823, she carried the United States Ministers to Spain and the Argentine Republic.
In 1824 Congress was placed in ordinary at Norfolk until December when she was towed to Washington for repairs. In November 1829, she returned to Norfolk where she served as receiving ship for several years and then was laid up in ordinary.
A survey in 1834 found her unfit for repair and she was broken up at the Norfolk Navy Yard by order of the Navy Commissioner.