The history of the journal goes back to 1994 when some collected scientific articles were published under the name Modeling and Analysis of Information Systems. Since then the edition has become annual, and the number of published issues per year increased from 2 up to 6. Today, it is a quarterly periodical. In 1999 the MAIS was registered as a mass media by the State Press Committee of the Russian Federation, and by the ISSN International Centre

In October, 2014 the results of the open competition for receiving the state support for Russian scientific journals development and their promotion into the international scientific information space were announced. Modeling and Analysis of Information Systems was among 30 winners (in all, 536 applications were submitted for the competition) and became one of two mathematical journals – the winners in the direction "Exact and Natural Sciences".