On May 9, 1919, the first meeting of the "Society for the Study of the Baikal Region" took place, during which the museum was founded. One of its first exhibits was the wall clock of Decembrist N. A. Bestuzhev, collected by him during his exile at the Petrovsky factory.

In 1921, the Baikal Regional Museum began operating in the building of the former Real School. In 1923, by the decision of the Buryat Revolutionary Committee under the leadership of M. N. Yerbanov, the museum was transformed into the Buryat-Mongolian National Museum, known as the Verkhneudinsk Local History Museum.

The museum opened its doors in early April 1924, placing its exhibition in three rooms. Its collection included exhibits from the Burvystkom and Pribgubvystkom, as well as items presented by the Buryat-Mongolian ASSR at the All-Russian Agricultural and Handicraft Exhibition. The collection was divided into three sections: cultural-historical, natural-historical, and socio-economic. From May 18 to September 15, 1924, the museum's funds increased by 1,199 items. In the fall of 1924, the museum began moving to the building of the former merchant's passage of merchant Vtorov.

From May 18 to 23, 1930, the first exhibition of banknotes and postage stamps in Buryatia was held at the museum, featuring up to 1,000 banknotes and 400 stamps.

On July 12, 1983, the Museum of Nature of Buryatia opened in Ulan-Ude, created based on the nature department of the Verkhneudinsk Local History Museum.

Since 2011, the museum has been part of the State Autonomous Institution of Culture of the Republic of Buryatia "National Museum of the Republic of Buryatia."