The council was established in 1958, a time at which most of the academic institutions were dependent on the governmental budget, and there was concern among academics that the government would politically influence higher education institutions.
In 1956 the government appointed a special committee, which was supposed to advise the government how to act, in order to assure that no ruling political party will be able to influence the academic institutions. The Governor of the Bank of Israel, David Horowitz, was the head of the committee, which advised the government to appoint a special apolitical and academic council which would supervise the functioning of the academic institutions and their relations with the government. Soon after, in 1958, the Knesset passed the Council for Higher Education Law, which established the organisation.