Prunk was born in the small village of Loka pri Zidanem Mostu near the town of Sevnica in central Slovenia, in what was then the German-occupied Lower Styria. He graduated from University of Ljubljana in 1966 and obtained his master's degree from the same institution in 1972. He obtained his PhD in 1976 with thesis on the relationship between the Slovenian Christian Socialist movement and the Communist Party of Slovenia within the Liberation Front of the Slovenian People, which at the time was a somehow problematic topic. In 1984 and 1988, he was awarded the scholarships by the Alexander von Humboldt Foundation, which enabled him to continue his studies in Cologne and Freiburg. Later, he worked as a researcher at the University of Freiburg. From 1966 to 1995, he collaborated with the Institute for modern history in Ljubljana. He worked as professor at the Faculty for Social Sciences of the University of Ljubljana.