The history of Gorno-Altaisk State University begins in 1949. In that year, according to the decision of the regional executive committee of the Council of Deputies of Workers, a Gorno-Altaisk teacher training institute was organized. It provided a two-year term of training for the preparation of pedagogical staff to serve in the Gorno-Altaisk autonomous region.

In the beginning there were only three departments at the institute (the Department of Language and Literature, the Physics and Mathematics Department, and the Department of Natural Geography). 130 students were enrolled there. A little bit later, the Department of Language and Literature was transformed into the History and Philology Department. In 1950, the fourth department - the Preparatory Department - was opened.

In 1951, the Chair of the Altai Language and Literature was formed within the History and Philology Department. Since the first years of its existence, the teachers, along with their pedagogical activities, have been engaged in research of topical problems of Altai philology, working out better techniques for teaching Altai language and literature in order to attract students to this work and prepare personnel for the institute.

In 1953, the Altai teacher training institute was transformed into Gorno-Altaisk State Teacher Training College (GATTC). GATTC began with three faculties (physical and mathematical, biological, and language and literature) and seven chairs: Marxism-Leninism, pedagogy, physics, mathematicians, natural sciences, language and literature, and the Altai language and literature. The institute also had physical laboratories (optics,┐ mechanics, electricity, warmth), a broadcasting center, laboratories and offices of botany, zoology┐, inorganic chemistry and qualitative analysis, Marxism-Leninism, pedagogy, language and literature, physical education, an educational workshop, and insignificant economic and educational stock (inventory).

According to historical records, in the 1954-1955 academic year, 40 faculty members, including one Doctor of Biological Sciences, two Candidates of Pedagogical Sciences, three Candidates of Physical Sciences, two Candidates of Physical and Mathematical Sciences, four Candidates of Biological Sciences, one Candidate of Chemical Sciences and one Candidate of Agricultural Sciences worked there.

In 1958, the Biology Department was transformed into the Natural-Geographical Department with specialities "biology-chemistry" and "geography-biology." The next change in the structure of the higher school occurred two years later: one more independent structural division, the Physical Training Chair, appeared at the institute. In 1959, the section of tourists was formed at the Physical Training Chair, which had grown by 1967 to the level of a tourist club ("Horizon").

The history of formation and development of the separate divisions is also connected with the history of the college, which left an appreciable trace in the memory of students and teachers of GATTC. The Department of Public Professions (DPP) became one of them. The purpose of its creation consisted in the preparation of future teachers for the organization of extracurricular creative activities, as well as for carrying out ideological and cultural-educational work. Many students who graduated from the Department of Public Professions could use their experience in different spheres and to become lecturers, critics, cultural organizers, photographers, Pioneer leaders, judges of athletics, instructors in tourism, librarians, and journalists. By 1969, the departments counted 29 sections total.

In 1963, the first students' scientific conference was held at the institute, resulting in the formation of a Scientific Student Society (SSS), which united in its structure sixteen scientific students' circles.

In 1985, the Natural-Geographical Department was divided into two independent departments: Biochemical and Geographical.

In 1989, the History and Philology Department was divided into two separate Philological and Historical Departments.

In 1991, the Department of Foreign Languages was established, and the vocational training of teachers of English and German languages began.

On June 20th, 1993 a governmental order provided for the creation of Gorno-Altaisk State University (GASU) on the campus of GATTC and Gorno-Altaisk Agricultural Technical School. By that time, six departments functioned at the university (geographical, biochemical, physical and mathematical, philological, historical, and the department of foreign languages), where 1978 full-time and 1219 part-time students were enrolled. 270 teachers, including 6 doctors of sciences and professors and 80 candidates of sciences and senior lecturers worked at 20 chairs.

In 1993, two new departments were formed at the university: agricultural (for the preparation of veterinary surgeons and scientific agriculturists for the Altai Republic) and economic (for the preparation of experts in the economic sphere). In 1998, the Economic Department was transformed into the Economy and Law Department, and in 2003 the law branch was separated into an independent structural division - the Law Department.

In 1997, the Pedagogy and Psychology Division was organized at the Geography Department, and in 2005 it was transformed into Psychology and Pedagogy Department.

The youngest department of the university is the Department of Social Management, formed in 2011.