With regards to the inefficiencies and uncompromising situations within the humanities and social sciences field in Iran, the challenge of problematizing these sciences is inevitable. So far, numerous research analyzing humanities and social sciences’ problems in the Iranian academic system have been published. Considering the important role of humanities and social sciences in the modern Iranian society, we attempt to suggest a theoretical framework for the problematization of humanities and social sciences in Iran. The exploration of the main challenges facing humanities and social sciences in Iran from the community, academy and administration point of view, sparks three hypotheses. First, humanities and social sciences’ theories and teachings are not applied accurately. Second, the humanities and social sciences’ schools of thought are not chosen properly according to Iranian circumstances. And third, there are metaphysical differences between axioms and presupposition of humanities and social sciences having western origins and those with Islamic-Iranian culture