The oldest university in the Northern Region was Kokchetav Pedagogical Institute, which was opened by Decree No. 563 of the Council of Ministers of Kazakh SSR on July 25, 1962.
The rector of the Institute was appointed the candidate of historical sciences, associate professor Gorokhvodatsky Ivan Stepanovich. There was only one unified faculty of philology, physics and mathematics at the university, where the training was conducted in three specialties: Russian Language, Literature and History, Russian Language and Literature for Kazakh Schools, Physics and Mathematics. Since August 1963, physico-mathematical and philological faculties began to function independently. According to Decree of Council of Ministers KazSSR of March 29, 1965 No. 241 Kokchetav Pedagogical Institute was named after the first Kazakh scientist-educator Chokan Chingizovich Valikhanov.
In 1972 with the retirement of Gorokhvodatsky I.S. the rector of Kokchetav Pedagogical Institute became the candidate of Philology, associate professor -Boyarsky Evgeny Ivanovich, and after him the Vice-rector for educational, scientific and educational work was appointed the candidate of Philological Sciences, Associate Professor -Zhulamanov K.D. In January 1984, a new teaching and laboratory building was opened for 2000 students, which allowed to increase the number of graduates in Kazakh and Russian languages. New specialties were opened later: Kazakh language and literature (1982), chemistry, biology (1984), fine arts and drawing (1985), computer science; new faculties: chemical-biological (1985), faculty for advanced training of principals (1979). The number of students increased from 400 to 2500.
In 1990, Candidate of Philosophy, assistant professor Kuandyk Dosmaganbetovich Zhulamanov was elected as rector of Ch. Valikhanov Kokchetav Pedagogical Institute, but in 1992 he was forced to leave his post for health reasons. Doctor of Physical and Mathematical Sciences, Professor Abai Ahmetgaliyevich Aitmukhambetov was appointed as the rector of Ch. Valikhanov Kokchetav Pedagogical Institute in 1992.In parallel with the training of teachers in the region, engineers were trained for developing industry and construction too. In 1963 in Kokshetau the general technical faculty of Pavlodar industrial institute was established, the first director of which was engineer Mikhail Fedorovich Rysikov.
In 1972, the general technical faculty of Pavlodar Industrial Institute was moved to Karaganda Polytechnic Institute. In 1987, a new academic building was opened for 1000 places. The training was conducted in the evening form on the specialties: "Industrial and civil construction", "Technology of machine building", "Automobiles and automobile economy".
The Specialty "Radio engineering" was opened in 1988.
Since 1990, the Faculty has opened a correspondence department, and in 1991 the first student’s admission for the full-time education in the specialties: "Economics and Management in Construction" and "Technology of Mechanical Engineering". With the support of mining enterprises, the specialty "Open Mining" was opened. Kokshetau branch of Karaganda Polytechnic Institute was organized on the basis of the general technical faculty in 1993. Candidate of Pedagogical Sciences, Associate Professor K. A. Aitkozhin was appointed as director. In 1995 took place the first graduate of full-time students.
On August 1, 1979, a branch of Tselinograd Agricultural Institute was opened in Kokchetav where the training of specialists in the specialties “Agronomy” and “Zootechnician” has began, and in the specialty "Mechanization of Agriculture" in 1980. The first director of the branch was Candidate of Agricultural Sciences, associate professor Isatay Galievich Temreshev. As a part of the branch there were 3 faculties. In September 1985, the branch was headed by Doctor of Economics, Professor Bakyt Gazizovich Zhunusov.
January 9, 1991 by decree of the State Agrarian Industry of the USSR this branch was transformed into Kokchetav Agricultural Institute, Zhunusov B.G. was appointed as the rector. The beginning of real processes of modernization of the system of higher education was the process of optimization of universities. By decree of the Ministry of Education of the Republic of Kazakhstan dated May 23, 1996, No. 143 Sh. Ualikhanov Kokshetau University was established on the basis of Kokshetau Pedagogical Institute named after Ch. Valikhanov including S. Sadvakassov Agricultural Institute and a branch of Karaganda Polytechnic Institute.
The first rector of the university was Doctor of Physical and Mathematical Sciences, Professor Abai Akhmetgalievich Aitmukhambetov. In 2001, according to decree of the Government of the Republic of Kazakhstan, Sh. Ualikhanov Kokshetau University was renamed into the Republican State Enterprise “Shokan Ualikhanov Kokshetau State University”.
During the first years of the university's work, the educational process was updated and modernized:
In 1998 MA course opening took place;
One of the first in the Republic University started introducing three-level system of training;
Since 2000 the higher education institution passed to rating system of an assessment of efficiency of educational and methodical work;
Since 2003 the training in credit technology began;
In 2005, one of the first universities to introduce a quality management system and successfully passed certification for compliance with international standards ISO 9001-2000.
In 2007, the doctor of philological sciences, professor Shakimashrip Ibraevich Ibraev was appointed as the rector of the university. Since December 2010, the rector of Sh. Ualikhanov KSU was appointed the Doctor of Technical Sciences, Professor Naiman Bubeevich Kalabaev. In 2012, according to Decree of the Government of the Republic of Kazakhstan (dated April 28, 2012, No. 544), the Republican State Enterprise “Sh. Ualikhanov Kokshetau State University” of the Ministry of Education and Science of the Republic of Kazakhstan was reorganized into the Republican State Enterprise on the right of economic use “Sh. Ualikhanov Kokshetau State University” of the Ministry of Education and Science of the Republic of Kazakhstan. From December 2012 to July 2014, the rector of the University was Doctor of Economic Sciences, Professor Yelubayev Sagintai Zekenovich. In July 2014, the rector of the University was appointed Doctor of Technical Sciences, Professor Abzhapparov Abdumutalip Abzhapparovich.
Since 2018, the university has been headed by the candidate of economic sciences Marat Kadiruly Syrlybayev.
By the order of Committee for State Property and Privatization of the Ministry of Finance of the Republic of Kazakhstan dated May 27, 2020 No. 319, “Sh.Ualikhanov Kokshetau State University” was reorganized into the non-profit joint-stock company “Sh.Ualikhanov Kokshetau University”.