ZAS grew out of the Central Institute for Linguistics (ZISW), which belonged to the Academy of Sciences (AdW) of the GDR. In 1992, after Germany's reunification, parts of this internationally renowned institute were incorporated in the Förderungsgesellschaft Wissenschaftliche Neuvorhaben, run by the Max-Planck-Society, and continued its work under the name Specialist Research Centre for General Linguistics, Typology and Universals Research (FAS). Following a recommendation of the German Wissenschaftsrat and with funding from the federal state of Berlin and from the German Science Foundation (DFG), the Centers for Advanced Study in the Humanities (GWZ) was founded in 1996. This is a larger organisation hosting not only ZAS but also the Centre for Literary and Cultural Research and the Centre for Modern Oriental Studies.

Professor Dr. Ewald Lang from Humboldt University in Berlin was the temporary director of FAS and became the founding director of ZAS. In 2001 Professor Dr. Manfred Krifka, also from Humboldt University, took over the position as the director of ZAS. The basic infrastructure is financed by the state of Berlin. Till the end of 2007, most funding of the research activities came from the German Science Foundation (DFG), granted in successive funding periods.

The German Wissenschaftsrat has recommended further funding for the GWZ and ZAS after 2007. Since January 2008, ZAS is funded by the state of Berlin and the Federal Ministry of Education and Research (BMBF) till the end of 2019. The research program, which comprises five project areas, is called Embedding, linkage and constituent boundaries in speech, grammar and discourse. The core research program is supplemented by further projects (funded, among others, by the German Science Foundation (DFG), the European Science Foundation and the Investitionsbank Berlin).

The scientific activites of ZAS are evaluated by an international advisory board, which gives an annual report to the state of Berlin and the BMBF.