After completing his PhD, he became an assistant and lecturer at Technical University of Munich (1965–1968). From 1968 to 1973, he was Professor and Director at Technical University of Hannover; then, he became a professor at Institute for Physical Chemistry, Ludwig Maximilian University of Munich (1973–1986). During the 1970s and 80s, he was also a visiting professor at the California Institute of Technology (1976–1977), the University of Wisconsin–Milwaukee (1979) and the University of California, Berkeley (1981–82).
He became the director at the Fritz Haber Institute of the MPG from 1986 till his retirement in 2004. In 1986, as honors, he was named "Honorary Professor" at the Free University of Berlin and at the Technical University of Berlin, and in 1996 at the Humboldt University of Berlin.
From 2008 to 2016, Ertl served as a member of the university council of Technische Universität Darmstadt.