Imam Khomeini pays special attention to reason and rationality in his system of thought. His works on Islamic sciences indicate how he attaches significance to rational reasoning and how he applies reason and rational methodology. Despite extremist rationalism, self-sufficiency and autarky of reason in understanding man, the realities of the world of being, spiritual perfection and salvation, and the ways and means to gain the two, Imam Khomeini believed in some constraints and impotence of reason. He was of the opinion that reason must be at the service of revelation, then it must be supported and led by religion and Sharia law. This research paper, developed through discretionary and document analysis method, studies constraints and impotence of reason in view of Imam Khomeini. The findings of this paper are the following: reason is incompetent in understanding the majority of realities, mysteries and codes of the universe such as the quality of revelation and prophethood, resurrection of the body, philosophy of Islamic precepts, etc. Since reason is directly affected by internal and external factors and situations, it is fallible to faults and trespassing reality in what it perceives, understands and figures out. If man shares reason with the realities on hidden acts of worship, he will end up with denying religious obligations and certainties of religion.