Aulis Joki received his doctorate of philosophy in 1953. He was a lecturer in Finnish at Stockholm University from 1951 to 1958 and from 1957 a researcher at the Suomen Research Institute and an associate professor at the University of Helsinki, where he served as professor of Finnish-Ugric linguistics from 1965 to 1977.

He became the world's leading expert on Samoyedic languages at an early stage and subsequently concentrated mainly on Uralic-Altaic and Indo-Uralic language contacts. In 1973 he published a groundbreaking monograph, Uralier und Indogermanen, which deals with earlier contacts between Uralic and Indo-European languages and peoples.
Joki also made a contribution as one of the editors of the etymological dictionary Suomen kielen etymologinen sanakirja and as a foster of a new generation of scholars.