The Archaeological Department is the oldest of the specialized museum departments in Slovenia. It acquires, stores, and studies material from all archaeological periods found throughout Slovenia. It also has a small collection of artifacts from Egypt, including a mummy. The earliest finds were acquired more than 170 years ago.

The Department of History and Applied Art keep records, collects, documents, preserved, studies, investigates, and displays museum exponents that present the stories of historical events, economic trends, everyday life, and artistic achievements, objects that bear information about the past. It offers the public a view into the historical periods that in part formed the present day reality of Slovenia and the Slovenes.

The Numismatic Cabinet is both the only and the central institution of its kind in Slovenia. From the very foundation of the museum it has systematically acquired and scientifically studied numismatic and other museum exponents important for the monetary, financial, and banking history of the Slovenian lands.

The Graphics Cabinet collects, preserves, and studies examples of the graphic arts and presents this material and information about it to the public.

The tradition of conservation and restoration of museum exponents in the National Museum extends into the 19th century, in the period of the first major excavations in Doljenska/Lower Carniola and Kranjska/Carniola. After the Second World War, the Conservation-Restoration workshop became an independent unit of the museum, and has remained the central workshop for all of Slovenia throughout this time.

The library functions today as a specialized library dealing with cultural affairs. The library has an official status as a public library and is open to local experts and foreign visitors, including a large number of students. For purposes of study, it is possible to view older material and printed matter of particular historical importance.