Archaeology, previously “Comparative Archaeology”, is the oldest discipline, as Oscar Montelius was already lecturing in this field in 1887–1893 at Stockholm University College (later to become Stockholm University) and it was established as a discipline in its own right in 1917. Its first professor was Nils Åberg (1940–1953).

Classical Archaeology and Ancient History was established in 1948, through grants collected to commemorate the birth of the Swedish author Viktor Rydberg. The first holder of the Viktor Rydberg Chair was Professor Gösta Säflund (1948–1969).

The Osteological Research Laboratory, later the Osteoarchaeological Research Laboratory, was founded at Ulriksdal Palace in 1967, partly through a royal donation. Its first professor was Nils-Gustaf Gejvall (1969–1977). Teaching in this field began in 1977.

The Archaeological Research Laboratory was established in Green’s Villa in 1976. Its first director was Birgit Arrhenius, professor of archaeological science, in 1986–1998.

The Stockholm Numismatic Institute is funded by the Gunnar Ekström Foundation for Numismatic Research. The first professor in this field, Brita Malmer (1979–1992), originally worked at the Royal Coin Cabinet, but was attached to Stockholm University from 1988 onwards.

The Centre for the study of Cultural Evolution is an interdisciplinary initiative at Stockholm University that was founded in 2007. The objective is to create an internationally competitive scientific environment for studies on the causal relationships that shape and change human culture.

The centre for Palaeogenetics was founded in 2019 between Stockholm University and Naturhistoriska riksmuseet, in order to create a centre for research based on ancient DNA.