The leader representing the Faculty is the Dean who reports to the Rector of the Charles University. Some of the specific tasks are delegated to the Vice-Deans. Together with representatives of other parts of the Faculty they form a pro-active advisory board – the Dean's Board.

The executive component, charged with the budgetary and administrative part of everyday activities, is the Dean´s Office. The individual Departments are responsible for e.g. organization of studies, budget, maintenance of the buildings and equipment. The daily business of the Dean's Office is coordinated in close collaboration with the Vice-Deans, the Bursar, who is responsible for the inner workings and budget of the Faculty. The Bursar reports to the Dean. Decision-making roles are played by two self-governing bodies of the Faculty – the Academic Senate and the Scientific Board. The Academic Senate is an elected body, representing the academic community; it develops long-term objectives for the Faculty. The Dean must gain approval of the Academic Senate for the new regulations, the annual budget, long-term objectives and other important documents.

The Academic Senate also approves the members of the Scientific Board, a self-governing body nominated by the Dean. The scientific board is composed of prominent scientists of the Faculty as well as external specialists. The Scientific Board approves the Study Programmes, debates the long-term conceptual matters of the Faculty, is involved in the promotion to the rank of Associate and Full Professors, and in general issues related to teaching and research at the Faculty.
For specific tasks, there are other boards as well as informal working groups. Most of these advisory bodies are nominated by the Dean, but some are also appointed by the Academic Senate, Scientific Board, or in collaboration with of all administrative boards. In a formal sense, most power lies in the Committees of the Academic Senate.