The history of this church is directly linked to the big fire that affected the Church of the Society of Jesus occurred on December 8, 1863, being the current church its successor. Its history is also linked to the vicissitudes suffered by the Jesuits in the territories colonized by the Spanish Kingdom in America, since by order of the King Charles III, the Society of Jesus order had to abandon the lands owned by the Kingdom in 1767. Besides, Pope Clement XIV suppressed the Society of Jesus in 1773. After all these problems, Jesuits returned definitively to Chile in 1848.

Next to the private school run by Jesuit order (Colegio San Ignacio), the church of the same name was built. Foundation stone was laid on December 15, 1867. Italian architect Eusebio Chelli worked on the construction of the main structure. He also designed the Recoleta Dominica and Augustine churches. The construction of the church was completed in 1872. By then, the church had not still the characteristic façade with two towers. It was blessed by Juan Bautista Mieges, Kansas City bishop, who was visiting the country by that time. In 1872 too, Eusebio Chelli left the project.

In 1899, two large 47-meter high towers were erected under the direction of the architect Eugenio Joannon. According to records, they were the first being built with an iron structure and cement lining. Later, Italian architect Ignacio Cremonesi worked on designing and building the façade and joining it to the two large towers.

Records indicate that the two Chilean Saints were directly related to this church. Saint Teresa of the Andes went to this church to attend Mass and be oriented in her spiritual vocation by Jesuit priests. Likewise, Saint Alberto Hurtado, a Jesuit priest, lawyer, social worker and writer, founder of the Hogar de Cristo Foundation, is also related to this church. He celebrated masses and gave confession to parishioners who attended with profound devotion from the wealthiest sector of Santiago.

This church was declared National Monument in 2002 for being in an area considered a Typical Zone and for conserving a variety of heritage treasures, both artistic and spiritual, as a part of the history of the order in our country.

The 2010 earthquake caused medium damages, mainly on stuccoes, cracks and crevices in some of its walls and broken decorative figures. For this reason, a restoration plan was generated, which was completed on July, 2011.