When the Protestant Theological Faculty was founded in 1919, it was the first opportunity for students to officially study Protestant theology in the Czech lands for centuries. Before the First World War, Bohemia had been part of Catholic Austria, and there had been many restrictions on Protestants. Candidates for the ministry had had to go to Vienna to study.
With the establishment of the new Czechoslovak state after the War came full religious freedom. Reformed and Lutheran Protestants united to form the Evangelical Church of Czech Brethren (ECCB), and one of the first things it did was to establish a Faculty of Protestant Theology so that its theology students and those from other churches could now be trained in Bohemia in the Czech language, with a study programme that took into account the specific Czech Protestant traditions of Jan Hus and the Czech Brethren. The Faculty (originally known as the Hus Czechoslovak Protestant Theological Faculty) was established as an independent institute of higher education by a law of the Czechoslovak Republic passed on 8 April 1919. Teaching started in October 1919 in modest surroundings in the sacristy of the Church of the Saviour in Prague, with only 14 students, but the Faculty soon moved to more suitable premises, and student numbers grew steadily. Women started studying at the Faculty in 1922; their number increased considerably after the Synod of the ECCB decided to ordain women to the ministry in 1953.
During the Nazi occupation in the 1940s the Faculty was closed down, along with most other institutes of higher education, but it resumed its activities when the Second World War was over. In 1950 the Communist state decided that the Faculty should be divided into two schools: the Hus Theological Faculty for students from the Czechoslovak Hussite Church, and the Comenius Protestant Theological Faculty for students from the ECCB and the smaller churches. Under the Communists the Comenius Faculty experienced many difficulties and the number of students dropped to below 100. For most of the 1950s and 1960s the Dean was the leading Czech Protestant theologian Josef Lukl Hromádka.
The fall of the Communist regime in 1989 meant new opportunities and many changes for the Comenius Faculty. In 1990 it was incorporated into Charles University and renamed the Protestant Theological Faculty. In 1995 it moved to larger premises on its present site in Černá Street. There was a tremendous increase in the number of students, meaning a move away from the earlier family atmosphere, and that some students now had no church background. An increasing emphasis was placed on research with a growth in the number of doctoral students. The opening of frontiers within Europe enabled the Faculty to intensify its international contacts and exchanges, so important for the small Czech Protestant community.
In the late 1990s new study programmes were opened up in Pastoral and Social Work and the Theology of Christian Traditions, and recently the Faculty has developed a successful Life-Long Learning programme for retired people and others interested in learning about theology. In 2019-20 there are some 550 students at the Faculty, including about 100 Life-Long Learning students. In spite of the many changes it has undergone during the 100 years of its existence, the Faculty still strives to follow its original calling and train students to examine critically the challenges of their time in the light of God’s Word and the Czech Protestant tradition.