Kearsarge departed Portsmouth, New Hampshire on 5 February 1862 for the coast of Spain. She thence sailed to Gibraltar to join the blockade of Confederate raider Sumter, forcing her abandonment in December. However, Sumter's commanding captain, Raphael Semmes, soon commissioned Confederate raider Alabama on the high seas off the Azores.
From November 1862 through March 1863 Kearsarge prepared for her fight with Alabama at Cadiz, then searched for the raider from along the coast of Northern Europe to the Canaries, Madeira, and the Western Islands. Arriving at Cherbourg, France, on 14 June 1864, she found Alabama in port where she had gone for repairs after a devastating cruise at the expense of the United States' merchant marine. Kearsarge took up patrol at the harbor's entrance to await Semmes' next move.
On 19 June, Alabama stood out of Cherbourg Harbor for her last action. Mindful of French neutrality, Kearsarge's new commanding officer, Captain John Winslow, took the sloop-of-war well clear of territorial waters, then turned to meet the Confederate cruiser.
Alabama opened fire first while Kearsarge held her reply until she had closed to less than 1000 yards. Steaming on opposite courses, the ships moved around a circle as each commander tried to cross his opponent's bow to deliver deadly raking fire. The battle quickly turned against Alabama, for the quality of her long-stored powder and shell had deteriorated. Kearsarge, on the other hand, had been given added protection by chain cable triced in tiers along her sides abreast vital places. One hour after she fired her first salvo, Alabama had been reduced to a sinking wreck. Semmes struck his colors and sent a boat to Kearsarge with a message of surrender and an appeal for help. Kearsarge rescued the majority of Alabama's survivors; but Semmes and 41 others were picked up by British yacht Deerhound and escaped in her to England.
Kearsarge steamed along the French coast in an unsuccessful search for CSS Florida, thence proceeded to the Caribbean before turning northward for Boston, Massachusetts, where she decommissioned on 26 November 1864 for repairs. She recommissioned 1 April 1865 and sailed on 14 April for the coast of Spain in an attempt to intercept CSS Stonewall, but the Confederate ram eluded Federal ships and surrendered to Spanish authorities at Havana, Cuba, on 19 May. After cruising the Mediterranean Sea and the English Channel south to Monrovia, Liberia, Kearsarge decommissioned 14 August 1886 in the Boston Navy Yard.
Kearsarge recommisioned 16 January 1868 and sailed 12 February to serve in the South Pacific operating out of Valparaiso, Chile. On 22 August she landed provisions for destitute earthquake victims in Peru. She continued to watch over American commercial interests along the coast of South America until 17 April 1869. Then she sailed to watch over American interests among the Marquesas, Society Islands, Navigators Islands, and Fiji Islands. She also called at the ports of New South Wales and New Zealand before returning to Calao, Peru, on 31 October 1869. She resumed duties on the South Pacific Station until 21 July 1870, then cruised to the Hawaiian Islands before decommissioning in the Mare Island Navy Yard on 11 October 1870.
Kearsarge recommissioned on 8 December 1873 and departed on 4 March 1874 for Yokohama, Japan, arriving 11 May. She cruised on Asiatic Station for three years, protecting American citizens and commerce in China, Japan, and the Philippines. From 4 September to 13 December 1874 she carried Professor Asaph Hall's scientific party from Nagasaki, Japan, to Vladivostok, Russia, to observe the transit of Venus. She departed Nagasaki on 3 September 1877 and returned to Boston 30 December via the Suez Canal and Mediterranean ports. She decommissioned at Portsmouth, New Hampshire, on 15 January 1878.
Kearsarge recommissioned 15 May 1879 for four years of duty in the North Atlantic ranging from Newfoundland to the Caribbean Sea and the coast of Panama. She departed New York 21 August 1883 to cruise for three years in Mediterranean, Northern European waters, and along the coast of Africa. She returned to Portsmouth on 12 November and decommissioned in the Portsmouth Navy Yard 1 December 1886.
Kearsarge recommissioned 2 November 1888 and largely spent her remaining years protecting American interests in the West Indies, off Venezuela, and along the Central Americas. She departed Haiti on 30 January 1884 for Bluefields, Nicaragua, but was wrecked on Roncador Reef on 2 February 1884. Her officers and crew safely made it ashore.
Congress appropriated $45,000 to raise Kearsarge and tow her home; but a salvage team of the Boston Towboat Company found that she could not be raised.
Kearsarge was struck from the Naval Vessel Register in 1884.
For other ships with this name, see USS Kearsarge