CEU and many of its 16 departments and schools have cooperation agreements with the following universities and research institutes in Hungary.

Andrássy University, Budapest, Hungary (AUB) – Cooperation agreement with the CEU Departments of International Relations, Legal Studies, History, Nationalism Studies and CEU Institute of Advanced Study http://www.andrassyuni.eu/

Eötvös Loránd University of Science (ELTE)-UNESCO Minority Program – Student exchange program with the CEU Department of Nationalism Studies

Human Rights Information and Documentation Centre (INDOK) - European master's program in Human Rights and Democratization (E.MA) students attend courses at the CEU Department of Legal Studies

Hungarian Institute of International Affairs - European Research Center - Academic cooperation (joint projects, applications, actions, papers, events, building of research networks, letting premises, cross-promotion) with the CEU Center for EU Enlargement Studies (CENS)

Institute for Legal Studies at the Center for Social Sciences of the Hungarian Academy of Sciences (MTA TK JTI) – General MoU with the CEU Department of Legal Studies

Institute of Mathematics of the Budapest University of Technology (BME) and Computer and Automation Research Institute of the Hungarian Academy of Sciences (MTA SZTAKI) - Cooperation agreement for student exchange, adjunct professors and advisers, joint research projects, joint events, sharing library resources with the CEU Department of Mathematics and its Applications

University of Szeged - Cultural heritage MA program (mutual teaching of courses, common projects, summer university, internship modules for students of the program) with the CEU School of Interdisciplinary Historical Studies