In 1930, the Jesuit mission was established in Šiauliai. In 1936, on the initiative of Benediktas Andruška (the first rector) a stone oratory was built. At that time, there was one priest and two brothers Jesuits. Until 1944, four rectors changed. They also acted as chiefs of the Jesuit mission.
In spring of 1948, priest Antanas Šeškevičius was exiled and the church was closed, turned into a warehouse, later, into a gym.
In 1986, pretending that there was a necessity to build a concert hall, the then city authorities received funding and started restoration of the church. In 1989, church music festival took place in it. In 1990, it was returned to believers and on December 23, consecrated.
On September 11, 1993, Pope John Paul II found peace and a shelter of rest here, blessing both the church and the future school. After two years, next to the church, in the former kindergarten, Father Benediktas Andruška primary school and community centre were founded.