As of August 21, 2018, the Museum of Prague has been registered on the list of research organizations. It conducts independent basic and applied research and publicly shares the results of its expert work by publishing activities, presentations at workshops and conferences, and organizing lectures and other educational activities. As a regionally focused museum, it primarily engages in interdisciplinary research in the context of Prague’s history. In the field of science and research, the Museum of Prague focuses primarily on the expert processing of collection items and the examining of the social, cultural, political, and economic phenomena to which these artifacts refer. To this end, it uses the knowledge and methods of history and archaeology, analytical approaches to collection conservation, and, not least, the latest digitalization and AI tools. In 2025, documentation and research focusing on nature in the Prague metropolitan area were added to the list of the Museum of Prague’s expert and educational activities. This new direction allows for a better understanding of the relationship between the urban environment and the natural processes taking place inside it.

The development of science and research at the museum is also linked to the ongoing support and expanding range of grant applications (GA ČR, OP JAK, TAČR, and Erasmus+ programmes).

In 2025, the Museum of Prague became an identity provider within the eduID federation. As a result, museum staff and users of the museum library gained access to domestic and international databases, repositories, and other information resources that require eduID authentication. This autumn, an agreement was signed with the National Library of the Czech Republic to provide access to the Kramerius database and the DNNT collection (Works Unavailable on the Market).