The Montana Archaeological Society (MAS) was founded in April, 1958 during the annual meeting of the Montana Academy of Sciences, held at Montana State University. The Bozeman campus was called Montana State College at that time. Francis L. Niven of Bozeman was elected the first president of the MAS and helped to promote the early ambitions of the group, namely the education and training of amateur archaeologists interested in working in the field. It was at the second meeting, held one year later at Carroll College in Helena, when the group began to discuss breaking away from the Montana Academy of Sciences altogether to officially create the MAS as a non-profit organization. MAS member Stuart Conner, a lawyer from Billings with a deep-rooted interest in archaeology, offered his services in drawing up the articles of incorporation and writing the by-laws under which the MAS would operate. In April of 1960 the Montana Archaeological Society met for the first time as a registered non-profit organization, fully independent from the Montana Academy of Sciences.

As a non-profit organization, the MAS sought first and foremost to encourage public interest in local and state history and to promote awareness of the unnecessary loss and destruction of that history through the construction of highways and dams, as well as the unfortunate looting of historic and prehistoric sites in the name of artifact collecting. The MAS worked hard from the beginning to utilize its membership base in lobbying the state government to protect archaeological sites by making the destruction and looting of historic or prehistoric sites punishable by law. The directors of the MAS also put a heavy emphasis on the need to establish parameters for archaeological research. The group saw the need for a standardization of educational doctrine and resources. One way the MAS decided to tackle this issue was through the publication of the journal Archaeology in Montana. The journal acted as a forum for the publication and conservation of field work and research, allowing educators and professionals, as well as students and other non-professionals, to keep up with current topics of interest in the fields of archaeology and anthropology.

Throughout the 1970s and 1980s, the mission of the Montana Archaeological Society was slowly reoriented from academia and education towards the varying roles and responsibilities of the archaeological field in a broader cultural context. With more archaeologists and anthropologists being employed by the government to oversee local and state heritage programs the question of ethics regarding the impact of archaeological research on Native American communities became a central concern. It was during this time when several professional members of the MAS decided that they needed to harness their collective interests and form a group consisting solely of professionals. It was in this way that the Montana Archaeological Association (MAA) began in 1980, working in tandem with the Montana Archaeological Society to advance the field of archaeology.

In 1996, the MAA, having never officially incorporated itself as an organization under Montana state law, elected to dissolve and to delegate all of its interests and activities to the MAS. Since the membership of both groups overlapped, the transition was smooth and the Montana Archaeological Society assumed all responsibility related to the sponsorship of Archaeology Week, as well as a more pronounced role in the political lobbying that had been such an important facet of the MAA. The two groups officially merged together after members approved the decision at their annual spring meetings in 1996.

The Montana Archaeological Society continues to meet annually to present research, discuss new trends in the field, and to elect its officers and directors. The group also continues to publish the journal Archaeology in Montana, and offers back issues of the journal which date back to its original publication in 1959.