Malayer University started in 1991 with 30 students of Educational Technology as Malayer Teacher Education Center. It was later developed and renamed to Malayer Higher Education Complex in 2000. Later, in 2005, It was promoted to Malayer University. Finally, after 16 years the main site of the campus was completed and officially inaugurated by the former speaker of the Islamic Parliament of Iran, Dr. Gh. Hadad Adel in 2007. Being a governmental organization, Malayer University is considered as one of the fastest growing universities in Iran and has developed its infra structure as well as research facilities very quickly. From beginning, there were only 7 departments till 2006 and now it has more than 6000 students within 6 faculties and two national research institutes, with a good number of Master Degree and Ph.D. students in more than 71 different disciplines. Currently, Faculties of Civil and Architecture, Engineering, Natural Resources and Environment, Science, Humanities and Agricultural Sciences and National Research Institutes of Grapes and Raisins and Nanotechnology are actively engaged in research and education in Malayer University.

Chancellors of Malayer University from establishment are:
1. Dr. H. Zamanian (2005 - 2010)
2. Dr. B. Amani (2010-2014).
3. Dr B.Hayati (2014-2017)
4. Dr M.Babaeipour (2017-2018)
5. Dr M.Maleki (2018)
6. Dr K.Sayevand (2018 till 2022)
7. Dr E.MohammadiManesh(2022 till persent )