The first Lithuanian Faculty of Theology and Philosophy was established in 1922 at the Lithuanian University (Lietuvos Universitetatas), renamed Vytautas Magnus University (Vytauto Didziojo Universitetas) in 1930. The Congregation for Catholic Education (for Seminaries and Educational Institutions) canonically approved the faculty in 1928 and granted it the right to confer degrees.
During the Soviet era between 1940 and 1990 the faculty was separated from the Vytautas Magnus University and continued its activities at the Kaunas Priest Seminary (Kauno kunigu seminarija) with the approval Congregation for Catholic Education (for Seminaries and Educational Institutions). The university faculty was re-established in 1990, followed by the merger of the Kaunas Priest Seminary and Vytautas Magnus University in 1994. They now function as the Faculty of Catholic Theology of Vytautas Magnus University (Kataliku Teologijos Fakultetas Vytauto Didziojo Universitete).
According to the agreement between the Holy See and the Republic of Lithuania (2000), Lithuania recognizes the degrees conferred by Kaunas Priest Seminary in the years 1940-1991.
Today, the faculty offers Bachelor programs in Catholic Theology and Pedagogy of Religion, a Licentiate program in Pastoral Theology, and Master programs in Religious Education, Family Research, and Pastoral Theology.