In 1910, after Dębniki had been incorporated into Kraków, Mayor Juliusz Leo and the City Council decided to build a parish church for the districts on the right side of the Vistula. In 1918, the Archbishop of Kraków, Adam Sapieha, set up a new pastoral post covering, among other things, the Dębniki district and entrusted it to the Salesian Society.

A wooden church was built in 1920, and when it became too small for the worshippers, it was decided in 1929 to create a new one, which was erected between 1932 and 1938 according to a design by the architect Wacław Krzyżanowski, author of designs for, among others, the building of the AGH University of Science and Technology and the Jagiellonian Library. The consecration of the church was attended by Karol Wojtyła, a student of Polish Studies, who was living in Dębniki in the house of his uncle Feliks Kaczorowski in the summer of 1938. He then took up residence in the parish from 1938 to 1944. In 1946, he celebrated his first Mass here with the faithful, and as Pope John Paul II he visited the shrine on 17 August 2002.

It is a modernist, single-nave church with a Latin cross plan. The nave is separated from the flatly closed chancel by a transept, and above its intersection with the nave rises the bell tower, which dominates the building and is 45 metres high and covered by an openwork dome topped with a cross. The windows are decorated with stained glass and the pillars with mosaics from the early 1980s.