In 1990, the government of the Federal Republic of Germany chose the University of California, Berkeley as one of the original three "Centers of Excellence" in the United States, along with Harvard and Georgetown, with the mission to foster American understanding of contemporary developments in Europe. The establishment of the "University of California Center for German and European Studies" (CGES), inaugurated in the presence of German Chancellor Helmut Kohl, was accompanied by a generous long-term grant from the German government with the contractual agreement that when the grant period ended in the year 2000, the Center would continue in its mission with the support of the University.
In 1999, the University established IES, unifying the staff, resources, and programs of UC Berkeley's Center for German and European Studies (CGES) and Center for Western European Studies (CWES), which housed the France-Berkeley Fund, French Cultural Studies Program, Finnish Studies Program, Italian Studies Program, Portuguese Studies Program, and Spanish Studies Program.
In 2009, IES and the Institute of Slavic, East European, and Eurasian Studies at the University of California, Berkeley established a European Union Center. The joint effort of these two Institutes was funded with a grant from the European Commission, in cooperation with the School of Public Health, the Institute of Governmental Studies, the Berkeley Roundtable on the International Economy, and the UC Berkeley School of Law.
In 2015, the Finnish Studies Program merged into a Nordic Studies Program and the Italian Studies Program was reestablished as the Program for the Study of Italy. The BENELUX Program was created. Following the visit to IES by President Michael D. Higgins of Ireland, an Irish Studies Program was created in 2016.
In 2017, the German Historical Institute opened its West Coast branch, GHI West, at IES. In cooperation with the Austrian Marshall Plan Foundation and the Federal Ministry of Science, Research, and Economy of Austria, IES also created a Program for the Study of Austria.