After studying computer science with a minor in communication sciences at the University of Bonn, Mattern became a VLSI design and parallelism researcher at Kaiserslautern University of Technology.
In 1991 Mattern was offered a teaching position at Saarland University in Saarbrücken; in 1994 he moved to the Department of Computer Science of the Technische Universität Darmstadt.
In 1999 Mattern responded to ETH Zurich's call for the establishment of a Ubiquitous Computing research group.
Mattern is also a co-founder of the common M-Lab Competency Center at ETH Zurich and the University of St. Gallen.
Together with Colin Fidge, he developed the vector clock algorithm, which allows one to generate a partial ordering of events in a distributed system and to detect causality violations.