The Medical University of Białystok was created in accordance to the terms of the Council of Ministers Ordinance of February 3rd, 1950, however, the initial activities for establishing the Medical University of Białystok occured at the beginning of 1949. The founding father of the University was Dr. Jerzy Sztachelski and Professor Tadeusz Kielanowski presided as the first Rector.

The main seat of the Medical University of Białystok was (and is still) located in the 18th century Branicki Palace, the most magnificent and precious historic structure located in Białystok. The first theoretical science departments were housed adjacent to the palace in Collegium Primum, and in the second year of existence the University obtained the right to confer scientific degrees. In 1953, the first clinical departments were created, and in 1954, Collegium Universum was built to house the majority of the theoretical science departments. In 1955, the academic journal, "Annals of the Medical University of Białystok", was issued for the first time and is still being published today. In 1956, another academic journal, "Medyk Białostocki", was briefly published before it prematurely discontinued. However, in 2000, the decision to resume publication of the “Medyk Białostocki” was made.

The State Teaching Hospital of the Medical University of Bialystok was opened in 1962 and in 1968 the Division of Dentistry was created. In 1977, the Faculty of Pharmacy with the Division of Medical Analytics was established, however, there was no initial recruitment until 1987, when the first group of students began their studies at the Faculty of Pharmacy with the Division of Medical Analytics. In 1982, Collegium Pathologicum was opened and the Children's Teaching Hospital began admitting patients in 1988. In 1999, Collegium Novum was opened, with the Division of Nursing also being created in that same year. In 20??, the Division of Medical Education in English was created and the inaugral class of the English-Language 6-Year MD Program began their studies in 2005.