The NSK Department of Pure and Applied Philosophy is concerned with classical philosophical issues and their anomalies. Its main topics of investigations are the question of God, and the essence and meaning of sexuality in relation to the absolute and evil, theonthology with psychoanalysis. The Department actively co-operates with other NSK groups.

The representative for the philosophical branch of NSK is philosopher and writer Peter Mlakar, who is best known for his speeches concerning religion and his very particular view on the manifestations of evil in contemporary society. His early speeches have been collated and published as Reden an die Deutsche Nation ('Speeches to the German Nation', Verlag Turia & Kant, Vienna, 1993). He has also published three philosophical works in the Slovene language: Spisi o nadnaravnem (Essays on the Supernatural, Analecta, Ljubljana, 1992), Uvod v boga (An Introduction to God, Zalo#ba NSK, Ljubljana, 1997, and published in Croatian, Zagreb, 2000), and Hribi in doline (Hills and Valleys, Zalo#ba NSK, 1999).

As one might expect, Mlakar’s style is declarative and bombastic, but his form of rhetoric also illuminates existential conundrums of the sort that most people prefer not to be confronted with. In response to 'Essays on the Supernatural', a well-known Slovene Catholic philosopher remarked that such a work 'cannot be opposed with counter-argument, but only with prayer and fasting.'