CERGE-EI has two main governing bodies. The Executive and Supervisory Committee (ESC), composed of renowned economists including international experts, CERGE-EI's tenured faculty, and representatives of Charles University and the Czech Academy of Sciences, primarily ensures that the highest academic standards are upheld. The Board of Trustees grants PhD in Economics and MA in Economics degrees under CERGE-EI's US permanent charter and makes faculty promotion decisions based on the recommendation of the ESC.

CERGE, Charles University and the Economics Institute (EI) of the Czech Academy of Sciences have their own governing bodies. CERGE's Scientific Council primarily reviews and advises on the institute's research and educational activities, and the Graduation Council regulates CERGE’s study programs and their organization. The Economics Institute governance structure comprises the Supervisory Board, which has a supervisory and advisory role, the Board of the institute which is the basic body of EI academics and researchers, and the Academy Assembly.