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Varna Medical University was established as a Higher Medical Institute in 1960. October 1st 1961 is accepted for its birthday– the first day of the first academic year in the first higher medical school in northeast Bulgaria. The establishment of the third higher medical school in Bulgaria is in response to the rising public needs for highly qualified medical staff and specialized medical assistance for the people of this region.

All departments and main clinics developed during the first 10 years. A training basis for educational, scientific and research work was established. Attention was paid mainly to the continuous improvement of the practical training. The expansion of the institute led to the building of new hospitals, both for training purposes and for the healthcare needs of Northeast Bulgaria. The Obstetrics and Gynecology Hospital, Psychiatric Hospital (the largest on the Balkans), Eye Hospital, the Therapeutic Hospital (current University Hospital "St. Marina"- Varna EAD) were built. 

The establishment of the Medical Academy in 1972 (until 1987) and the inclusion of all Bulgarian higher medical institutions in its structure provided new opportunities for development. In 1978 the affiliate faculty was founded in Dobrich (Tolbuhin) for medical training (3rd to 6th year students). The Higher Medical Institute – Varna grew as a major center for medical staff education, for scientific research and innovations, for therapeutic, diagnostic, consultative, organizational and methodological assistance. The institute possessed valuable and modern equipment.

In 1995, by a decree of the National Assembly, the Higher Medical Institute of Varna was renamed to Medical University of Varna. In 2002 the University accepted as its name the name of its patron – Prof. Dr. Paraskev Stoyanov. The university auditoria are traditionally named after prominent professors from the Medical University of Varna.

In 1993/1994, the training in the specialty “Health Care and Social Management” was launched preparing in advance the future staff for the implementation of the Bulgarian health care reform

In 2001, the Faculty of Public health was founded by a Decree of the Council of Ministers. 

In 2002, Varna Medical University won the "International Gold and Silver Award for Quality" in Mexico City.

In 2004 in Maastricht, Varna Medical University was approved for a full member of the most prestigious international associations – European University Association.

The youngest and the most modern Faculty of Dental Medicine on the Balkans opened its doors in 2006.

The Medical University of Varna is among the first members of the Black Sea Universities Network (BSUN) and is full member of the European University Association (EUA). From 2006 the graduating doctors receive a European supplement to their diplomas which is valid for their professional realisation in the EU countries.

The Laboratory of Nutrigenomics was established in 2007 within a project funded by the Ministry of Education, Youth and Science and possesses the latest equipment for molecular and biological research.

The new Faculty of Pharmacy was opened in 2008. With the establishment of the two new faculties – the Faculty of Dental Medicine and the Faculty of Pharmacy, Varna Medical University acquired the full structure of traditional higher school for training in the so-called "regulated professions". 

In 2008, for the first time in South Eastern Europe, a new elective course in maritime medicine was initiated at the Faculty of Medicine which is taught in the developed countries.​​​

Since the beginning of the 21st century, with the opening of new faculties and programmes, high-tech laboratories, research centres, creation of more conditions for scientific exchange, work on programmes, active international cooperation, scientific periodicals, better online presence and work in the new digital environment, university TV, MU-Varna has expanded its educational scope and has developed further its academic potential.