In 1962 Pavilionis graduated from a night-school for workers in Šiauliai. He attended the school at night after finishing his work at a bicycle factory. The same year he was admitted to the Vilnius University to study foreign languages. In 1968 he graduated the university with a degree in philology. From 1968 to 1971 he continued postgraduate studies at the Science Academy of Ukraine and earned doctor's degree in logic. Pavilionis then returned to Lithuania and joined Vilnius University as member of the faculty (1971–1977 docent, 1982–1990 professor). For some time he was the head of the Department of History of Philosophy and Logic.