Well-known Deccan Education Society (DES) manages Fergusson College. At the college the Local Managing Committee is constituted according to the Maharashtra Universities Act of 1994. All other committees are given responsibility to look into management of various parts/matters of the college. The details of this aspect are described in Management page.

The Principal of the college heads both the academic as well as the administrative sections and is overall in charge of the college. Vice Principals are appointed to assist the Principal in smooth functioning of the administration system and to enable the smooth conduct of academic programs.

College office mainly looks into the matter related to admissions, eligibility, and examinations. It also provides clerical support required for maintaining records and for interaction with government, university, parents and students.

Various committees in the College help in monitoring and facilitating several administrative functions and thus make administration open and transparent.