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A previous brick church stood on this site, but was destroyed in the Earthquake and Fire of 04/18/1906. The architectural firm of Shea and Lofquist did a large number of churches for the Catholic Archdiocese in San Francisco and elsewhere in CA. This chapel opened 12/25/1918. Unlike its brick predecessor, the architects reinforced this structure with steel and reinforced concrete.

Originally, this church, like those of the mendicant Franciscan order, were often devoid of much ornamentation. It had simple, Romanesque windows, and planar stucco wall surfaces. The lantern provided some decorative flair, lit by quatrefoil windows, a favorite decorative pattern of Mission Revival architects. In its basic form, the San Francisco lantern recalled that of the Pazzi Chapel, (1429-1461), designed by Filippo Brunelleschi (1377-1446) for the Franciscan church of Santa Croce in Florence, Italy. The basilica's original plan was cruciform. Its flamboyant Spanish Baroque entryways and front portal came later.

Period-correct Churrigueresque ornamentation was added to the second basilica in 1926. This effort at reproducing historically correct Spanish Baroque ornamentation became a trend for churches in the 1910s and 1920s. Bertam Grosvernor Goodhue's buildings at San Diego's Panama-California Exposition (1915), elaborate renditions of Spanish Renaissance and Baroque precedents, set the trend for historically accurate ornamentation. The completion of the highly visible Saint Vincent de Paul Church in Los Angeles, CA, (1923-1925) may also have been an influence on the Archdiocese in San Francisco to add this detailing. The latter church was designed by Goodhue's former partners, the Boston, MA, firm of Cram and Ferguson, in association with Los Angeleno A.C. Martin, Sr., (1879-1960).