CEU was founded in 1991 to support the democratic transitions in Europe and Central Asia. Today, CEU includes 4 schools, 13 departments, and 15 research centers focusing on contemporary challenges of building open societies. CEU is the exclusive beneficiary of a permanent endowment fund, one of the largest academic endowments in Europe.

Incorporated in the State of New York, Central European University is organized as an American graduate institution, governed by a Board of Trustees. The Board of Trustees has general charge of the affairs, property and assets of Central European University. The Senate establishes, approves or initiates academic programs and establishes academic and admission standards. The Academic Forum comprises department, program and unit heads, who make recommendations on academic matters for consideration by the Senate. The Senior Staff oversees the coordination and control of the university's daily operations and ensures adequate strategic planning in cooperation with the appropriate university forum. The President and Rector is the overall academic and administrative head of the university. The Office of the Provost and Academic Pro-Rector is responsible for overseeing academic issues related to departments, faculty and students. 

In Hungary, CEU is recognized as a Hungarian private higher education institution under the name Közép-európai Egyetem (the Hungarian name for Central European University).