It is under the administration of Naval Base Coronado. It is 21 miles (34 kilometers) long and has a land area of 147.13 km2 (56.81 square miles). According to the census, 148 military and civilian persons were estimated to be living on the island in 2018. The island is also the inspiration for the city of San Clemente in Orange County, California.

Signs of human occupancy around San Clemente Island that date back 10,000 years have been discovered by archeologists.

Later residents left trade materials from the northern islands as well as the mainland, including Coso obsidian from the California desert, which was discovered in the desert of California. It has not been determined which tribe the most recent occupants belonged to, although the Tongva, who have a lengthy history on Santa Catalina Island, are the most plausible candidates based on historical evidence.

The Chumash, who occupied the northern Channel Islands at the time, could have had an impact on the locals. Battle relics such as “the skeletons of hundreds of men stacked one atop another” were discovered on the islands of San Clemente and San Nicolas, as well.

After sailing around the world in search of treasure, Juan Rodrguez Cabrillo discovered the island and christened it Victoria. On November 23, 1602, the feast day of Saint Clement, the Spanish adventurer Sebastián Vizcaino discovered the island and nicknamed it after himself. In the nineteenth century and into the twentieth century, ranchers, fishers, and smugglers used it to transport their goods.

While under Captain Josiah B. Whippey (or Whipple) command of the whaleship Elbe off of Poughkeepsie, New York, in 1835, the ship fished for sperm whales all the way up to “St. Clements Island” (San Clemente Island). It was here that the American steamship Lansing as well as the steam-schooner California were berthed to process blue, fin, and humpback whales caught by their “killer boats” (steam-driven whale catchers) from 1926 to 1930, and from 1933 to 1937, respectively, in Pyramid Cove on the southern side of San Clemente Island. The Norwegian factory ship Esperanza caught blue whales as far north as San Clemente Island in 1935, according to historical records.