The UEMA originated at the Federation of Higher Schools of Maranhão - FESM, created by Law 3260 of 22 August 1972 to coordinate and integrate isolated establishments of higher education system of Maranhao. The FESM initially consisted of four units of higher education: School of Management, School of Engineering, School of Agriculture and School of Caxias. In 1975 FESM entered the School of Veterinary Medicine in St. Louis and in 1979 the Faculty of Empress of Education.
The UEMA was later reorganized by Law No. 5,921, of March 15, 1994, and 5931, to April 22, 1994, as amended by Law No. 6663 of 04 June 1996. At first, the UEMA was linked to State Department of Education. After the administrative reform implemented by the State Government, in 1999, SEDUC was transformed into the State of Human Development Management - GDH. The UEMA was detached from GDH by State Law No. 7,734, of 19.04.2002, which provided new changes in the administrative structure of government, and joined the Management of State Planning and Management.