Spanish missionary Pedro Font scouted the site in March 1776 during Juan Bautista de Anza's expedition to establish a presidio on San Francisco Bay. The missionaries named their church San Francisco de Asis, after Francis of Assisi, founder of the Franciscan Order. It became known as Mission Dolores after the nearby Arroyo de Nuestra Senora de los Dolores, Our Lady of Sorrows Creek. On October 9, 1776, Fathers Francisco Palou and Pedro Benito Cambon dedicated a small chapel. Members of the local Ramaytush Ohlone tribe are recorded as entering the mission by 1785. Construction of the adobe church began in 1788, and the building was finished in 1791 with four-foot-thick walls designed to withstand both weather and time.

The mission's records tell a grim story alongside the spiritual one. Over 5,000 Native Americans died from disease and other causes at Mission San Francisco during the Spanish and Mexican periods. Between 1806 and 1816, thirty indigenous girls between nine and nineteen years old, recorded as monjas, died while living in the monjerio, the dormitory for single women. In 1817, the Franciscans established Mission San Rafael as an asistencia, essentially a satellite hospital, because conditions at Mission Dolores were killing the indigenous population. After Mexico gained independence from Spain in 1821, the Mexican government moved to free the Native Americans under mission guardianship. The Secularization Act of 1833 forced the missions to sell their commercial properties. By 1842, only eight Native Americans remained at the mission.

The California Gold Rush transformed the mission's surroundings. Plank roads connected downtown to the Mission District, which became a popular entertainment area. The Franciscans sold or leased remaining land to developers who built saloons and gambling halls. By 1876, a large Gothic Revival brick church had been built next to the adobe chapel to accommodate growing congregations. Then the 1906 earthquake struck. The brick church was destroyed. The adobe chapel was damaged but survived, its thick walls proving their worth across more than a century. To save the complex from the advancing fire, firefighters dynamited the convent and school across the street. Architect Willis Polk restored the adobe building in 1917, and a new basilica designed in the Churrigueresque style opened in 1918.

Today the mission complex includes the 1791 adobe chapel, the 1918 basilica designated a minor basilica by Pope Pius XII in 1952, a historic cemetery with grave markers dating from 1830 to 1898, and gardens featuring native plants from the original period alongside an Ohlone Indian ethno-botanic garden. The basilica contains a stained-glass window of Francis of Assisi created by German artist Franz Xaver Zettler. A cast-stone statue of Junipero Serra by Arthur Putnam, completed in 1909 and installed in 1918, stands on the grounds. The mission gave its name to the neighborhood, the park, the district, and in a sense, to the city itself. San Francisco de Asis became San Francisco. The adobe walls that Ohlone hands built still stand, painted ceiling and all, the oldest building in a city that has never stopped rebuilding everything around it.