The Faculty of Theology at the Kraków Academy (now Jagiellonian University) was first established at the request of Queen Jadwiga and her husband Jagiełło.

Throughout the existence of the Kingdom of Poland and further, during the partitions, and after the return to independence in 1918, most rectors of the Kraków Academy were drawn from theologians, who would become its most prominent personalities.

However, the Vatican issued a decree in 1959 stating that the Faculty of Theology "remains under the supervision of one ecclesiastic authority and in the future is to be formed according to the laws passed by the Apostolic see".

[2] In 1974 owing to the efforts of Cardinal Karol Wojtyła, the Archbishop of Kraków and future Pope John Paul II, the Faculty was bestowed the honourable title Pontifical.

On 19 June 2009 by virtue of the decision of Pope Benedict XVI[5] the Academy became the Pontifical University of John Paul II.