In the Spring of 1903, Bishop Thomas James Conaty took over as the bishop of the diocese of Los Angeles. In his first months as bishop, Bishop Conaty outlined a plan to expand the churches in Los Angeles. He quickly acquired a land to build a cathedral and three new parishes—Saint Thomas the Apostle, Saint Patrick and Saint Agnes. For St. Thomas, three lots were purchased in August 1903 at the southwest corner of Pico Boulevard and Hobston Street.

The land acquired for St. Thomas was in a desirable and expanding residential section of the city then known as "Pico Heights" to the southwest of Downtown Los Angeles. The first mass for the new St. Thomas the Apostle parish was held on August 16, 1903 in the chapel of the Immaculate Heart Convent in Pico Heights. An old Methodist church structure was purchased in late 1903 or early 1904 to serve as a temporary parish church until construction of a new church could be completed. Within a few months of the formation of the parish, Father John J. Clifford was appointed as the first pastor, and Father Murphy became it's deacon.

On the 12th of June, 1904, the corner-stone for the new church was laid in a ceremony conducted by Bishop Conaty. Six months afterwards, on December 1904, the church structure was completed and was opened on Christmas Day 1904 and the formal dedication ceremony for the church occurred on February 19, 1905.