Prunk has been actively involved in politics. As an early admirer of Jože Pučnik, he joined the Slovenian Social Democratic Union after the democratization of Slovenia. He was an active member of the Slovenian Democratic Party (known as Slovenian Social Democratic Party between 1989 and 2003). Between 1992 and 1993, he served as Minister for Slovenes outside Slovenia in the first coalition cabinet of Janez Drnovšek. Between 2004 and 2008, he served as chairman of the Party's internal Committee for Education Policies; he quit for disagreements over the Government policy favouring private universities. He became very critical of the then prime minister Janez Janša, whom he accused of being a "liberal with an authoritative touch" who aspires at becoming a "Slovenian Piłsudski".