Freedom is a very complex concept. It arises from the need for development, growth and social co-existence for the larger good of society. Institutions and systems of governance are created for that purpose. Individuals engaged in the institutions by their nature and functions acquire the level of freedom to carry out the object and functions of the institutions. Systems of governance are created to ensure the objective and orderly functioning of the institutions for the purpose for which institutions have evolved over time or created. Academic institutions have evolved over millenniums as the knowledge has evolved and has influenced the growth and development of the rest of the social institutions including the system of governance and self-governance in a static and dynamic manner. Often conflict arises when perceptions and visions of nature and functions of the institutions and individual engaged in it are blurred or one institutional set up tends to acquire undue authority over the other institutions again in the name of larger good for a larger number. Academic institutions acquire a special position in the domain of institutional framework of social institutions. The special position is acquired owing to the nature and functions of institutions as it is a mother of all the professions and social institutions including its own. It has, therefore, to have the freedom to dynamically evolve and be self-governed and be a critique of the rest of institutions and be its own critique again in the social institutions’ framework. The questions, therefore, arises how this complex concept of freedom is operated, self-managed or manages other institutional sets up evolved and created for the betterment of society. The chapter attempts to raise a few questions and tries addressing them in the context of academic freedom and institutional autonomy to self govern and be governed by other institutional frameworks.