The islands constitute one of the two exposed parts of the Kerguelen Plateau (the other being Heard Island and the McDonald islands), a large igneous province mostly submerged in the southern Indian Ocean. The main island, Grande Terre, is 6,675 km² (2,577 sq mi) in area, about three-quarters of the size of Corsica, and is surrounded by a further 300 smaller islands and islets, forming an archipelago of 7,215 km² (2,786 sq mi). The climate is harsh and chilly with frequent high winds throughout the year. The surrounding seas are generally rough and they remain ice-free year-round. There are no indigenous inhabitants, but France maintains a permanent presence of 45 to 100 soldiers, scientists, engineers, and researchers. There are no airports on the islands, so all travel to and from the outside world is by ship.

The islands were officially discovered by the French navigator Yves-Joseph de Kerguelen-Trémarec on 12 February 1772. The next day, Charles de Boisguehenneuc landed and claimed the island for the French crown. Yves de Kerguelen organised a second expedition in 1773 and arrived at the "baie de l'Oiseau" by December 1773. On 6 January 1774 he commanded his lieutenant, Henri Pascal de Rochegude, to leave a message notifying any passers-by of the two passages and of the French claim to the islands.

Thereafter, a number of expeditions briefly visited the islands, including the third voyage of Captain James Cook in December 1776. Cook verified and confirmed the passage of de Kerguelen by discovering and annotating the message left by the French navigator.

Soon after its discovery, the archipelago was regularly visited by whalers and sealers (mostly British, American, and Norwegian) who hunted the resident populations of whales and seals to the point of near extinction, including fur seals in the 18th century and elephant seals in the 19th century. The sealing era lasted from 1781 to 1922 during which time 284 sealing visits are recorded, nine of which ended when the vessel was wrecked. Modern industrial sealing, associated with whaling stations, occurred intermittently between 1908 and 1956. Since the end of the whaling and sealing era, most of the islands' species have been able to increase their population again. Relics of the sealing period include try pots, hut ruins, graves and inscriptions.

In 1800, the Hillsborough spent eight months sealing and whaling around the islands. During this time Captain Robert Rhodes, her master, prepared a chart of the islands. That vessel returned to London in April 1801 with 450 tons of sea elephant oil.

The islands were not completely surveyed until the Ross expedition of 1840.

The Australian James Kerguelen Robinson (1859–1914) was the first human born south of the Antarctic Convergence, on board the sealing ship Offley in Gulf of Morbihan (Royal Sound then), Kerguelen Island on 11 March 1859.

In 1874–1875, British, German, and U.S. expeditions visited Kerguelen to observe the transit of Venus. For the 1874 transit, George Biddell Airy of the U.K. Royal Observatory organised and equipped five expeditions to different parts of the world. Three of these were sent to the Kerguelen Islands and led by Stephen Joseph Perry, who set up his main observation station at Observatory Bay and two auxiliary stations, one at Thumb Peak led by Sommerville Goodridge, and the second at Supply Bay, led by Cyril Corbet. Observatory Bay was also used by the German Antarctic Expedition, led by Erich Dagobert von Drygalski in 1902–1903. In January 2007, an archaeological excavation was carried out at this site.

In 1877 the French started a coal mining operation, but soon abandoned it.

In 1892, due to German operations in the area, France sent the aviso Eure, under Commander Lieutard, to reassert its claim over the Kerguelen Islands, the islands of Amsterdam and St. Paul, and the Crozet Archipelago. In 1924, it was decided to administer these territories (in addition to that portion of Antarctica claimed by France and known as Adélie Land) from Madagascar; as with all Antarctic territorial claims, France's possession on the continent is held in abeyance until a new international treaty is ratified that defines each claimant's rights and obligations.

In 1908, the French explorer Raymond Rallier du Baty made a privately funded expedition to the island. His autobiographical account of the adventure (15,000 Miles in a Ketch. Thomas Nelson and Sons: London, 1917) describes the months that he spent surveying the island and hunting seals to finance his expedition.

The German auxiliary cruiser Atlantis called at Kerguelen during December 1940. During their stay the crew performed maintenance and replenished their water supplies. This ship's first fatality of the war occurred when a sailor, Bernhard Herrmann, fell while painting the funnel. He is buried in what is sometimes referred to as "the southernmost German war grave" of World War II.

Kerguelen has been continually occupied since 1950 by scientific research teams, with a population of 50 to 100 personnel frequently present. There is also a French satellite tracking station.

Until 1955, the Kerguelen Islands were administratively part of the French Colony of Madagascar and Dependencies. That same year, they collectively became known as Les Terres australes et antarctiques françaises (French Southern and Antarctic Lands) and were administratively part of the French Département d'outre-mer de la Réunion. In 2004 they were permanently transformed into their own entity (keeping the same name) but having inherited another group of five very remote tropical islands, les îles Éparses, which are also ruled by France and are dispersed widely throughout the southern Indian Ocean.