The Protestant Theological Faculty (originally known as the Hus Czechoslovak Protestant Theological Faculty) was founded in Prague on 28 April 1919.
Before the First World War, there had been many restrictions on Protestants in the Czech lands (which were part of Catholic Austria at the time) and candidates for the ministry had to go to Vienna to study. With the establishment of the new Czechoslovak state after the World War I. came full religious freedom. Reformed and Lutheran Protestants united to form the Evangelical Church of Czech Brethren, and one of its first actions was to establish a Faculty of Protestant Theology to train its theology students and those from other churches.
In the first year of its existence the Faculty had 14 students, but this soon grew to 78 in 1923 and 160 in 1929. Women started studying at the Faculty in 1922; their number increased considerably after the Synod of the Evangelical Church of Czech Brethren decided to ordain women to the ministry in 1953.
During the German occupation 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 1949-50 there were 230 students. 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 Evangelical Church of Czech Brethren 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.
After the fall of the Communist regime in 1989, new opportunities opened up for the Comenius Faculty. There was a tremendous increase in the number of students. In 1990 the Comenius Faculty was incorporated into Charles University and renamed the Protestant Theological Faculty.
In 1995 it moved to larger premises on its present site. In 1999 a new study programme in Pastoral and Social Work was opened in cooperation with the Catholic school Jabok. More than half the students at the Faculty are now enrolled on this programme, and in 2013 a new Department of Pastoral and Social Work was established to assume full responsibility for it.
In 2018-2019 the Faculty had around 500 students and some 35 teaching staff.