The laboratory of electro-modeling was organized in May, 1952 under the Petroleum expedition of Azerbaijan Academy of Sciences(AS) and served as the beginning of the creation of the Institute. In 1956, because of the reorganization of Petroleum expedition the Laboratory of electro-modeling has been included into the structure of the Institute of Physics and Mathematics of AS, and since 1958 it was transferred into the structure of the Institute of Mathematics and Mechanics and called Computer Center (CC).
At the end of 50s, the appearance of universal digital computers in Azerbaijan stimulated researches on numerical methods and programming. As a matter of this, in 1960 CC was extracted into an independent organization in the system of AS of the Republic. In the same year the computer laboratory was created in the structure of CC. This was the second one, after Ukraine, among the former Soviet republics, which played the main role in the development of Cybernetics, computer science and other engineering sciences. In 1965 CC was reorganized into the Institute of Cybernetics.
Department of the “Computer Aided Control Systems» created in 1971 in the structure of the Institute was extracted from the Institute in 2002 into an independent Institute of Information Technologies. The current Special Design Office "Cybernetics" was created at the Institute in 1978. In April 2014, by the decree of the Cabinet of Ministers, the Institute of Cybernetics of ANAS was renamed as the "Institute of Control Systems".