The department was lead since its foundation by Otakar A. Funda. In years 1995-1998 the Department was headed by Miloš Havelka who was succeeded by Miroslav Pauza. The Department of Philosophy is led by Anna Hogenová since 2001.

Philosophy is currently a separate field of study at the Faculty and it is possible to combine it with Hussite Theology, Orthodox Theology and Jewish Studies in Bachelor as well as Master Study Programs. Philosophy is a traditional prerequisite for studying Theology. This is why the Department collaborates with other theological departments in teaching theological subjects.

The objective of studying Philosophy at the Hussite Theological Faculty is to look into the development of philosophical thought from antiquity to present regarding Philosophy in Christian, Jewish and Islamic tradition. Students study Phenomenology, Hermeneutics, Logics and Ethics and thanks to their knowledge of classical languages they are able to read and analyze some philosophical texts in the source language. The members of the Department are concerned with Corporal Philosophy and corporeality, Phenomenology in modern Philosophy, Czech Philosophy, Philosophy of Religion, Ethics and Logics.