Prunk started going to primary school in his birthplace. After fourth grade, he shifted to the school in nearby Radeče. He continued his secondary education at Gymnasium in Celje. Graduating from history and sociology at the University of Ljubljana in 1966. He was recruited into Yugoslav People's Army in Sisak, Socialist Republic of Croatia in the years 1966/67. He obtained his master's degree from University of Ljubljana in 1972. In 1976, he obtained his PhD with a thesis on Slovenian Christian Socialist movement 1918-1941, which was still a controversial topic at that time. Prunk was awarded scholarships by the Alexander von Humboldt Foundation. He worked as a researcher and visiting professor at the University of Freiburg in 1984/1985 and 1994/1995, and in 1988/1989 at the University of Cologne.