Omsk State Medical University is one of the oldest universities of Siberia; it was founded in 1920 as the Medical Faculty of the Siberian Institute of Veterinary Medicine and Zoology which enrolled 186 students. In 1921, West Siberian State Medical Institute was established; and Prof. N.K. IVANOV-EMIN was assigned as the first rector. In 1924, it was renamed into Omsk State Medical Institute.

In autumn 1931, the Maternity and Child Protection Faculty was established which later was reorganized into the Pediatric Faculty. The Sanitary and Hygienic Faculty was founded in 1938 (now it is the Preventive Medicine Faculty). In 1957, there was the admission for the Dentistry Faculty. The fifth faculty established was the Faculty of Pharmacy which started to enroll students in 2002. In 1994, the Institute was granted with the status of State Medical Academy. On the 5th of December 2011, Omsk Medical College was affiliated with Omsk State Medical Academy.  In 2015, the Academy was assigned with the status of University.