The Ecumenical Institute of the Protestant Theological Faculty of Charles University concentrates on research into theology, spirituality and missiology, as these have been formed in confrontation as well as in dialogue between various Christian churches, and in modern times with secular and post-secular societies. It looks at both the history of these relations and their contemporary forms and possibilities. Among the areas of research and teaching in which the Institute engages are the following: the comparison of the approaches of different traditions to theological and practical questions; investigation of the ways in which the relation to Christian tradition as a common heritage and joint way ahead has changed, and how against this background relations between the Christian East and West have formed and are being formed; how unity in diversity and diversity in the understanding of unity have found and find echoes in ecumenical documents and their interpretations; and how all this has helped and helps the cultivation of a Christian spirit and Christian way of life in a plural, globalised world.

The Ecumenical Institute was founded in January 1956 as part of the Department of Systematic Theology (then under the direction of Josef Lukl Hromádka for the study of ecumenical questions and the organization of inter-church relations both at home and abroad. After 1989, under the direction of Prof. Pavel Filipi, professor of practical theology, the Ecumenical Institute was linked to the Department of Practical Theology. The Ecumenical Institute has been led by Prof. Ivana Noble as a self-standing institute of the faculty since 2016.