It was established in 1888, having originally been conceived around 1850 and expanded in 1913 by the Czech architect Karel Pařík adding four symmetric pavilions that contain the departments of archaeology, ethnology, natural history, and a library.

[1] After being closed for several years due to heavy damage during the Bosnian War, the museum has re-opened and is in the process of mounting new and pre-existing exhibits.

Having remained open for its entire history including during the Bosnian War in the early 1990s, the museum was closed between 2012 and 2015 due to disagreements about funding.

In 1913, the museum building was expanded by the Czech architect Karel Pařík who designed and added a structure of four symmetric pavilions with a facade in the Italian Renaissance Revival style.

Greatly influenced by the orientation of 19th-century European science heuristics and culture, the museum's collection under Hörmann grew rapidly especially in the departments of natural history and archaeology.

After the end of the war in 1918, which was followed by the first union of the South Slavs, the museum resumed its operations under the administration of what was then called the Kingdom of Serbs, Croats and Slovenes, which was later known as Yugoslavia.

Culture was declared to be of special importance for society by the Socialist Government and this period in time marked some of the National Museum's highest achievements in scientific research and publishing activities and exhibitions.

(See the publications[5]) During this period, was significant the contribution of Museum's Natural departments in the development of the Movement “Science to Youth" – Alliance of Young Researchers of Bosnia and Herzegovina.

The War in Bosnia and Herzegovina in 1992–95 not only ended the prolific activity of the National Museum, but it directly caused structural damage to the building.

Several students chained themselves to a pole in the lobby and remained inside, declaring they would stay there until the museum reopened, while dozens of others held a sit-in in front of the building.

[20] The Natural History Department covers the flora and fauna and the geology of Bosnia and Herzegovina and elsewhere, consisting of around 2,000,000 specimens collected from field research, exchange, gift or purchase.

[22] The Ethnology Department is responsible for collecting, preserving, exhibiting and studying all aspects of the material, spiritual and social culture of the peoples of Bosnia and Herzegovina.

It contains about 250,000 publications (journals, periodicals, books, newspapers) in the fields of archaeology, history, ethnology, folklore, mineralogy, geology, botany, zoology and museology.

[29] The Herald of the National Museum of Bosnia and Herzegovina (Bosnian: Glasnik Zemaljskog Muzeja Bosne i Hercegovine) is the oldest scientific journal in the country, with a first issue published on 1 January 1889.