The cave paintings found near San José del Cabo suggest that the region was inhabited since ancient times.

Later, the Pericú tribes settled on the peninsula. They were strong men who named the region Añiuti.

Cortés first visited the area in 1535. Subsequently, the port was used as a refuge for galleons returning from the Manila route and was then known as Aguada Segura and San Bernabé.

During this time, it was a place frequently visited by pirates. In the 17th century, European missionaries arrived and established missions. In 1730, the Mission of San José del Cabo was founded by the visiting father José Echeverría and the Jesuit father Nicolás Tamaral. However, colonization was not very successful, as the missionaries brought diseases that significantly decimated the population.

Along with the pirates, some whalers started arriving at Los Cabos, and fishing became the main economic activity in the region.

In the town of San José del Cabo, under the leadership of Fernando de la Toba, the Independence of Mexico was sworn and proclaimed for the second time in 1822 in the Territory of Baja California. 

In 1847, during the American invasion, the defense of Mexican territory took place in the town of San José del Cabo, and Lieutenant Antonio Mijares was heroically killed in battle. 

San José del Cabo began its activities as the municipal headquarters of the municipality of Los Cabos in 1928.

At the beginning of the 20th century, a tuna canning plant was built in Cabo San Lucas. This plant closed in the late 1960s, and since then, tourism has been promoted. 

In the 1940s and 1950s, the place was known to some people who arrived with their yachts for fishing, and since then, the tourist infrastructure has grown, making it one of the most well-known places worldwide.

In 1981, the State Congress approved the creation of the fourth Municipality of Los Cabos.