Prugovečki was born in Craiova, Romania to a Romanian[citation needed] mother, Helena (née Piatkowski), and Croatian father, Slavoljub.
He completed the first four years of secondary education in Bucharest, before his family was forced to relocate to Zagreb in 1951, due to an anti-Yugoslav campaign by the communist authorities.
He joined the Department of Theoretical Physics at the Institute Ruđer Bošković in Zagreb, where he worked as a research assistant until 1961.
He wrote his doctoral thesis under the direction of theoretical physicist Arthur Wightman, and earned his PhD from Princeton in 1964.
In 1974, he spent one year as a visiting professor at the Centre national de la recherche scientifique in Marseille, France.