The foundation of the Estonian Museum of Natural History was laid by naturalists of the XIX century.

The museum of the Estonian Literary Society (ELS), founded in 1842 and renamed into Provincial Museum in 1864, was active also in natural scientific research among its key areas of activity. This gained particular importance since 1872, when Alexander von der Pahlen (1820—1895), who was keen on natural sciences and therefore contributed to collecting the relevant materials, was elected chairman of the ELS.

A new section for studying the local natural environment was established at the museum in 1876 under the leadership of Alexander von der Pahlen, geologist Alexander Keyserling and academician Friedrich Schmidt. The need for establishing a separate museum of natural history was also considered. The idea was not realised but essentially a separate natural sciences section was nonetheless created.

The scientific collections of the museum began to grow rapidly, mainly through donations, and the growth was still further accelerated after the exhibitions were opened. The most significant collection acquired during this period is the collection of mounted birds inherited from Dr. G. A. von Rauch. The possessions were kept and displayed in rental premises until 1911, when the section moved to a building purchased in Kohtu Street. It was envisaged that the Provincial Museum would be developed section by section, yet only the natural sciences and art collections could count as separate sections at the time. The research carried out within the Estonian Provincial Natural Sciences Section, especially the geological research, attracted attention even abroad.

During World War I, the collections of the Provincial Museum, too, were in danger of being moved to Russia. The plans failed due to the museum’s passive resistance. Thus, the Provincial Museum in Tallinn was luckier than the Museum of the University of Tartu, whose possessions have still not been fully returned to Estonia.

During the period of the Republic of Estonia, the museum continued to operate under the Arts and Heritage Department of the Ministry of Education. Since 1926, it carried the name Museum of the Estonian Literary Society (former Provincial Museum), thus returning to its original name of 1842. The section of natural sciences carried the name Natural Sciences Section of the ELS since 1920. This change of name marked the extension of the section’s activities to cover “anything worth knowing from across the world”.

The Molotov-Ribbentrop Pact (1939) brought an end to Baltic-German institutions in Estonia. Most of the members of the ELS resettled to Germany and the ELS terminated its activities.

After the occupation of Estonia in 1940, the Soviet authorities declared all museums nationalized. The National Museum of Natural History was established to store the natural scientific possessions of the Provincial Museum. The new museum was to focus first of all on educational work and serve the wider public.

The National Museum of Natural History was established in Tallinn on 1 January 1941 by a Regulation of the Council of People’s Commissars of the Estonian SSR. The first member of its scientific staff and also the acting director was zoologist Eerik-Madis Kumari, a 1940 graduate of the University of Tartu.

The museum acquired approximately 19 500 geological, 55 500 botanical and 15 000 zoological specimens from the collections of the Provincial Museum. Over 10 000 of these were destroyed by a bomb hit in 1942.

The exhibition was re-opened in 1946. The entrance was free and with the first 3 months there were over 8000 visitors. Charicaristic to the time, the exhibitions carried ideological and political themes, for instance "The Stalinistic Reshaping Plan for the Nature" (1951). In the 1950s and 1960s museum employees took acively part of the pioneer camps, where they arranged tours, quizzes and theme days. 

The annual mushroom exhibition was started by the head of the botanical collections Gustav Vilbaste in 1946.

During the soviet period the museum started to feel a need for advertising with the ambition to educate as many people as possible. News about the openings of new exhibitions were published in important newspapers and in 1951 a commercial screen was used in the cinema "Oktoober". In the end of the 1940s the museum started to hold lectrues and meeting in the factories and schools to engage more grownups.

From that period to this day, the Estonian Museum of Natural History has grown to a museum with about 50 000 annual visitors. The museum collections include botanical, geological and zoological collections, it houses numerous events every month and welcomes hundreds of school children every week.