The Faculty of Medicine is one of the founding faculties of the University of Cologne, along with the Faculty of Philosophy, the Faculty of Law and the Faculty of Theology. Although the foundation charter of the High School was signed by Pope Urban VI, the initiative did not come from the emperor or a prince, but from the council of the Free Imperial City of Cologne, which also assumed the costs of teaching.

In 1388, Pope Urban VI signed the foundation charter of the university in Perugia, the fourth oldest university foundation in the late medieval German Empire after Prague (1348), Vienna (1365) and Heidelberg (1386). While many other universities owe their establishment to the initiative of important rulers, in Cologne, the old Colonia Agrippinensium (the former Oppidum Ubiorum - the dwelling place of the Ubians - declared a colonia - or city under Roman law - in 50 AD under the Roman Emperor Claudius from the family of Augustus), it was the citizens of the city who established the university.

The faculty was already highly regarded by students and professors in the early modern period.

As one of the founding faculties of the "universitas" - the unifying community of teachers and students in Cologne - Cologne's Faculty of Medicine, after an eventful history at the end of the 18th century, could look back on a considerable reputation - students and scholars from many famous faculties were enrolled here - as well as a teaching corpus of 13 lecturers, 8 of whom were full professors, and around 60 students. Under the leadership of the last deans, the otherwise rather conservative repertoire of courses was even supplemented by the subject of "children's diseases", which was still very rarely represented in German-speaking countries at the time. In addition to this, materia medica, chemistry, pathology, medical practice, anatomy, physiology, surgery, obstetrics and special lectures on forensic medicine and natural history were also covered during the three-year course. 15 years later, Goethe would praise Cologne University for its "excellent teachers" in the Faculty of Medicine.

In 1798, the "Old University" was closed by Napoleon and was replaced by the Cologne Central School, the "L'université de Cologne organiseé en école centrale", which continued teaching in the old, formerly ecclesiastical buildings on Marzellenstrasse up to and including September 1804.

After the "Old University" was abolished by Napoleon in 1798, the "New University" was opened in 1919 - again by the city council; the "Academy of Practical Medicine" and the clinic "auf der Lindenburg" were among the key founding elements. 

In 1919, the University was re-founded by the City Council, initially with the Faculty of Economics and Social Sciences, but then followed by the Faculty of Medicine (which emerged from the first "Academy of Practical Medicine" in the German Empire, founded in 1904). It was not until 1954 that the sponsorship was taken over by the state of North Rhine-Westphalia.

The conduct of the Cologne Medical Faculty during National Socialism was essentially similar to that of other faculties at the University of Cologne: highly deserving colleagues and academics were forced to retire or emigrate from 1934 onwards without any recognizable resistance from the institution with its conservative nationalist stance. 24 doctoral graduates were stripped of their medical doctorate. As a result, German university medicine lost touch with international developments in many areas. Resistance to Gleichschaltung and the influence of the party was limited to individual, mostly private actions. From 1934 to 1945, the deans were appointed directly by the rector in accordance with the Führerprinzip. Individual institutes and clinics pursued ideology-oriented science - especially in the fields of racial hygiene, castration and brain research. Military service by professors and lecturers as well as war damage dramatically impaired teaching and patient care and led to the clinics being completely outsourced. 

In 1954, the state of North Rhine-Westphalia took over sponsorship of the university. In the field of medicine, too, the academic focus has always been closely linked to political developments and social challenges. This is reflected both in the focus of research and in the further development of academic teaching.

Today, the Faculty of Medicine at the University of Cologne is considered one of the most popular locations in Germany among prospective students and enjoys an excellent reputation both nationally and internationally with more than 60 institutes and clinics as well as cooperating institutions.

Albert Dietrich (1873 - 1961): 1919 - 1920
Paul Frangenheim (1876 - 1930): 1920 - 1921
Reiner Müller (1879 - 1953): 1921 - 1922, 1928 - 1929
August Pröbsting (1860 - 1944): 1922 - 1923
Ferdinand Zinsser (1865 - 1952): 1923 - 1924
Franz Külbs (1876 - 1964): 1924 - 1925
Otto Tilmann (1862 - 1934): 1926 - 1927
Otto Siegfried Karl Johann Veit (1884 - 1972): 1927 - 1928
Gustav Aschaffenburg (1866 - 1944): 1929 - 1930
Rudolf Grashey (1876 - 1950): 1931 - 1932
Ernst Leupold (1884 - 1961): 1932 - 1933
Friedrich Bering (1878 - 1950): 1933 - 1934
Hans Kleinschmidt (1885 - 1977): 1935 - 1937
Hans Naujoks (1892 - 1959): 1937 - 1938
Hans Lullies (1898 - 1982): 1938 - 1941
Alfred Güttich (1883 - 1948): 1930 – 1931, 1942 - 1945
Josef Schüller (1888 - 1968): 1925 - 1926, 1945 - 1946, 1950 - 1951
Karl vom Hofe (1898 - 1969): 1946 - 1947, 1952 - 1954
Ernst Klenk (1896 - 1971): 1947 - 1948
Carl Bennholdt-Thomsen (1903 - 1971): 1948 - 1949
Hans Schulten (1899 - 1965): 1949 - 1950
Werner Scheid (1909 - 1987): 1951 - 1952
Matthias Hackenbroch (1894 - 1979): 1954 - 1955
Karl Friedrich Schmidhuber (1895 - 1967): 1955 - 1957
Leonhard Bernhard Seiferth (1899 - 1990): 1957 - 1958
Wilhelm Tönnis (1898 - 1978): 1958 - 1959
Carl Kaufmann (1900 - 1980): 1959 - 1960
Friedrich August Lentze (1900 - 1986): 1960 - 1962
Hans Friedrich Zipf (1911 - 1969): 1962 - 1963
Max Schneider (1904 - 1979): 1963 - 1964
Norbert Schümmelfeder (1916 - 1965): 1964 - 1965
Rolf Ortmann (1913 - 1994): 1965 - 1966
Georg Heberer (1920 - 1999): 1966 - 1967
Wilhelm Schink (1916 - 2004): 1967 - 1968
Rudolf Wolfgang Johannes Gross (1917 - 2008): 1968 - 1969
Hans Hirsch (1921 - 2004): 1969 - 1970
Gerd Klaus Steigleder: *1925: 1970 - 1971
Albrecht Stammler (1918 - 2009): 1971 - 1972
Robert Fischer (1930 - 2015): 1973 - 1974
Gerhard Pulverer *1930: 1974 - 1975
Werner Kaufmann (1924 - 2013): 1975 - 1976
Friedrich Wilhelm Klußmann: *1929: 1976 - 1978
Hans Hermann Hilger (1928 - 2022): 1978 - 1979
Rudolf Voß *1926: 1979 - 1980
Achim Bolte (1928 - 1997): 1980 - 1981
Heinz Pichlmaier (1930-2019): 1981 - 1982
Hansjürgen Hirche (1929-2014): 1982 -  1983
Michael Staak (1933-2019): 1983 - 1984
Wolfgang Klaus *1934: 1984 - 1985
Harald Dalichau *1934: 1985 - 1986
Wolf Isselhard (1930-1998): 1972 - 1973, 1986 - 1991
Walter Rüßmann *1939: 1991 - 1995
Conrad A. Baldamus (1940-2024): 1995 - 1997
Gerhard Krüger (1936-2020): 1997 - 2000
Gerd Lehmkuhl *1948: 2000 - 2004
Edgar Schömig *1960: 2004 - 2006
Joachim Klosterkötter *1946: 2006 - 2011
Thomas Krieg *1949: 2011 -2019
 

Gereon R. Fink *1964: since 2019 (2nd term of office started in 2023)