The Vice-Chancellor, who is the principal executive officer of the University, is appointed by H.E. the President of Sri Lanka for a period of three years. The Vice-Chancellor is responsible for the execution of policies & measures approved by the Council and the direction, supervision and control of the University. He is also responsible for the maintenance of discipline within the University.

The Deputy Vice-Chancellor is appointed by the Council of the University for a period of three years. The Deputy Vice-Chancellor shall at all times act on the directions and instructions of the Vice-Chancellor and assist the Vice-Chancellor in the exercise, performance and discharge of the powers, duties and functions conferred or imposed on or assigned to the Vice-Chancellor by the Universities Act or by any appropriate instrument.

The Deans are the academic and administrative heads of faculties, and are elected by the respective Faculty Boards from among the Heads of the Departments of study comprising each Faculty, including the incumbent Dean. Their term of office is three years. The Registrar is a full-time officer of the University and is appointed by the University Council. Subject to the direction and control of the Vice-Chancellor, the Registrar is responsible for the general administration of the University and the disciplinary control of its non-academic staff. The Registrar is also the custodian of the records and property of the University, and is the assistant accounting officer of the University.

The Librarian is a full-time officer of the University and is appointed by the Council. Subject to the direction and control of the Vice-Chancellor, the Librarian is responsible for the administration of the libraries of the University.

The Bursar is a full-time officer of the University and is appointed by the Council. Subject to the direction of the Registrar, the Bursar is responsible for the administration of the finances of the University. He is also the custodian of funds of the University.

The Directors of Postgraduate Institutes, who are the principal executive officers and the principal academic officers of the Institutes, are appointed by the University Grants Commission for a period of three years. They are ex-officio members and chairpersons of the Boards of Management and ex-officio members of Boards of Study.

The Authorities of the University of Peradeniya are:

(i) Council

(ii) Senate

(iii) Faculty Boards.

The Council and the Senate form the conventional two-tier pattern of University organization. The Council is the chief executive body and the governing authority of the University. The Senate is the academic authority and makes recommendations to the Council regarding teaching, research, examinations and related matters of the University. Next in rank are the Faculty Boards of the Faculties at the University of Peradeniya. Each Faculty Board regulates matters pertaining to teaching, research and examinations in the respective Faculty, subject to control of the Senate