The Faculty of Theology of the Pontifical University of John Paul II in Krakow (formerly the Pontifical Academy of Theology in Krakow) has taken over the traditions of the Faculty of Theology of the Jagiellonian University in Cracow, which date back to January 11, 1397 when Pope Boniface IX issued the bull Eximiae devotionis affectus authorizing the establishment of the Faculty of Theology at the above mentioned University.

In I974, thanks to the efforts of then Cardinal Karol Wojtyła, the Faculty of Theology was granted the honorary Papal title. Another significant event in the history of the Faculty was the publication by Pope John Paul II of the motu proprio Beata Hedvigis, on December 8, 1981, under which the Pontifical Academy of Theology in Krakow was established, consisting of three faculties: Theology, Philosophy, and Church History.

Finally, on the feast of the Sacred Heart of Jesus on June 19, 2009, Pope Benedict XVI, wishing to honor the memory of his predecessor - St. John Paul II - raised the Pontifical Academy of Theology to the dignity of the Pontifical University of John Paul II in Krakow, thus opening a new chapter of honor for the oldest Faculty of Theology in Poland.