Archaeology studies were introduced into the Faculty of Arts of Masaryk University by Emanuel Šimek in 1930, when the Department of Prehistory and Protohistory was established. Prof. František Kalousek became the Head of the department in 1958 and renamed it to the Chair of Prehistory and Ethnography, since 1961 to the Chair of Prehistory. Under his direction, the permanent field research stations at Pohansko near Břeclav and Těšetice-Kyjovice were founded. The amenities were intended for systematic training of students in all procedures of archaeological field research. In the basement floor of building C an archaeological laboratory was established, where students under the supervision of a laboratory technician carried out laboratory treatment of the finds from excavations.
The Chair Holder since 1970 was associate professor Bořivoj Dostál, who significantly contributed to the development of technical and scientific background of the excavations at Pohansko near Břeclav. In the laboratory also the restoration of valuable grave goods from Great Moravian graves (mainly jewellery) was practised.

Due to the ongoing normalisation process in the society, associate professor Dostál was replaced in his function of the Chair Holder already two years later by Radko Martin Pernička, who led the department until 1986. In this period, the number of staff and admitted students was reduced and many research and methodological trends had to be involuntarily abandoned. In 1977 the Chair of Prehistory merged with Chair of Museology. The three-year period 1986 – 1989 still deepened the stagnation of development of the study field, which was caused by ideological restriction of research goals and limitation of free contact with foreign scientists. The only exception was the orientation on archaeology of the Soviet Union. The independent Chair was dissolved and continued its existence as a department of the Chair of History of USSR and Socialist Countries.

Prof. Bořivoj Dostál was again installed as the Head of the renewed Chair already on 1 January 1990. The following four years led to significant renaissance of methodological approaches, revival and development of contacts with foreign researchers and restoration of the high scientific level of university excavations. These changes of course positively influenced the teaching and education of future archaeologists. At that time, the Department of Archaeology published among other outputs also the key compendium Pravěké dějiny Moravy (Prehistory of Moravia, 1993), edited by Prof. Vladimír Podborský. He became the Department Head in 1994 – 1998. The support in this period was oriented on the development of a second university field research station in Těšetice – Kyjovice, and organisation of many conferences and meetings of prehistoric archaeologists. Scientific workers of the Department of Archaeology and Museology collaborated in many international grant projects. Thanks to activities of associate professor Zdeněk Měřínský, the education in medieval archaeology, which has been omitted in the Czech Republic until that time, was integrated into the curriculum and was gradually extended. These efforts resulted in 1996 in the opening of another permanent university field research in Rokštejn Castle, which has been carried out continuously to this day, except a break in 1998. The gap in practical training was herewith filled and students are now made familiar with archaeological excavation in all its usual forms (multicultural prehistoric settlement on loess in Těšetice, complex hinterland of a fortified early medieval centre on sandy soils and in the riparian woodland, and specific stratigraphy of a defunct castle residence).

Prof. Zdeněk Měřínský led the Department of Archaeology and Museology since 1999 until 2015. Integral parts of the Department became in 2004 the Department of Classical Archaeology and in 2009 the Department of Prehistoric Archaeology of the Near East with its own field research in Syria. In 1999, the Department of Archaeology and Museology entered a six-year research programme of the Ministry of Education, Youth and Sports “The Centre for Archaeological Research into Social Structures from Prehistory until the High Middle Ages” (1999 – 2004), which was followed by another seven-year research programme “Interdisciplinary Centre for Research into Social Structures from Prehistory until the High Middle Ages“ (2005 – 2011). Significant impulses for innovation and development of pedagogical activity came from the grant projects by the Czech Science Foundation GA ČR “Moravian-Silesian School of Archaeological Doctoral Studies” (2006 – 2008), Moravian-Silesian School of Archaeological Doctoral Studies II (2009 – 2011) and a grant project within the Operational Programme Education for Competitiveness (OP EC) “Education in Modern Methods of Archaeological Practice” in 2009 – 2012. This grant project was followed in a far wider scope by another OP EC project “Innovation of Archaeology and Museology Education for Practice in the Interdisciplinary and International Frame”, which is mainly targeted at the development of e-learning, education on practical implementation of new methods, education on presentation forms and development of international and interdisciplinary cooperation of all departments within the Department of Archaeology and Museology (2012 – 2015). In 2013 – 2016, the Department of Archaeology and Museology acted as the principal investigator in the Programme for Applied Research and Development of National and Cultural Identity NAKI (DF13P01OVV005) “Historical Landscape Use in the Bohemian-Moravian Highlands in Prehistoric and Medieval Times”. The project was realised in cooperation with the Mendel University in Brno, Institute of Archaeology of the Czech Academy of Sciences in Brno, the company Archaia Brno, and the Museum of Vysočina Region in Jihlava. Important project outputs are besides specialised publications also certified methods of care for historical monuments. Another recent significant partner projects are the interdisciplinary project of the Grant Agency of Masaryk University GA MU “Relationships between Man, Climate and Vegetation in Pre-Industrial Landscape on Various Spatial Scales (CLOVEG)”, which was realised in cooperation with Faculty of Science MU (2015 – 2017) and the international project GA ČR “Frontier, Contact Zone or No Man’s Land? The Morava-Thaya Region from the Early to the High Middle Ages” which was realised in cooperation with the Institute of Prehistoric and Historical Archaeology, University of Vienna (2015 – 2017). The Head of the Department of Archaeology and Museology is since 2016 Prof. Jiří Macháček.

The existence of the Department of Archaeology and Museology was connected since the beginning with significant personalities of science and research.