The church is located in the city center, right next to Šiauliai Boulevard. During his visit to Lithuania on September 7, 1993, Pope John Paul II blessed the church as well as the future Jesuit school. The Jesuits follow the motto, “Everything for the greater glory of God.”  Often, devoting themselves to the grace of God, they would undertake various difficult tasks – missions or educational activities. The Jesuit monastery in Šiauliai was established in 1930 under the care of priest Benediktas Andruška (the first rector). The public oratory was built in 1935. In 1949, the church and monastery of St. Ignatius were closed. A warehouse and later a sports hall was installed in the church. It was returned to the congregation in 1990.

In commemoration of the 20th anniversary of Pope John Paul II’s visit to Lithuania, a monument was erected in the church yard. The path from the boulevard to the statue of the pope was named after Pope John Paul II.  

When Pope John Paul II was kneeling in the church of St. Ignatius of Loyola, his cassock was smeared with paint, and a red stain was noticed on the sculpture erected near the church, exactly where the pope’s cassock was stained. The people of Šiauliai call this event a miracle.