On March 4, 1920, the board of the Krasnokokshaysky district department of public education decided to create a Central Museum in Krasnokokshaysk. Just on April 3 of the same year, the museum opened its doors to visitors in a building on Sovetskaya Street, 32. On October 17, 1921, the board of public education of the Mari Autonomous Region decided to transform the district museum into a regional local history museum. The head was appointed F. E. Egorov, a teacher of the Mari language and ethnography at the Mari Pedagogical College.

The museum was located in the building of the pedagogical college, but in 1922, state support ceased, and the museum was closed. All exhibits were transferred for safekeeping to the ethnographic department of the college. The museum resumed operations on December 5, 1924, temporarily remaining in the ethnographic office of the college.

Upon the recommendation of the congress of teachers of the Mari Autonomous Region, a teacher, Timofey Evseevich Evseev, was sent to the museum, who began collecting ethnographic materials among the Mari people.

In 1925, the museum was named the Central Mari Museum. In early 1927, it was moved to a separate small stone building. By 1930, the museum occupied a one-story stone structure, where exhibition halls were located in three rooms.

In June 1932, the museum moved to the building of a closed church, where it managed to hold a short-term exhibition. After a major renovation of the church building in 1934, conditions were created for restoring the historical value of the museum, and a floor was equipped for an art gallery.

The museum collaborated with the Moscow Central Museum of Ethnography, the Vyatka Institute of Local History, and the Helsinki Ethnographic Museum in Finland.

Since February 1934, Timofey Evseev became the director of the museum. After the transformation of the Mari Autonomous Region into the Mari ASSR, the museum came under the jurisdiction of the People's Commissariat for Education of the Mari ASSR. In 1937, the museum moved to a new building. On January 20, 1939, the museum reopened after reorganization with departments of nature, history, and socialist construction.

From 1941 to 1946, the museum was temporarily closed, and its funds were transported and stored in a small stone room of the collective farm in the Ronginsky district of the Mari ASSR.

In 1946, the museum was named the Mari Scientific Local History Museum and came under the Management of Cultural and Educational Institutions of the Council of Ministers of the Mari ASSR. At that time, the current two-story building was allocated to the museum.

In the same year, archaeologist P. N. Starostin and the deputy director for scientific work B. V. Babushkin created the first scientific exhibition on archaeology, and in 1969, the exhibition "Nature of the Mari ASSR" was developed by N. V. Ivanov.

In 1975, an exhibition titled "Mari Folk Art" was held in Tartu, Estonian SSR, featuring over 200 exhibits. In 1987, for the first time abroad, in the city of Sombathely, Hungarian People's Republic, the museum organized an exhibition "Mari Folk Art," the exhibits of which were donated to the Museum of History of Sombathely.

At the initiative of director M. B. Matukova, by the decree of the Government of the Republic of Mari El dated August 4, 1992, the museum was renamed the National Museum of the Republic of Mari El, receiving the status of "national" and the name of its founder Timofey Evseev.

In 2003, the museum was renovated.

In February 2007, the 120th anniversary of Timofey Evseevich Evseev's birth was celebrated. New exhibitions were created: "Rituals of the Life Cycle: Traditional Culture of the Mari People of the 19th and 20th Centuries," "The Amazing World of Animals. Especially Protected Natural Areas of the Republic of Mari El," "Pages of the History of the Mari Region from Ancient Times to the 1980s."

In December 2014, for the research project "Caravan Exhibition 'Three Totems,'" employees of the ethnography department of the museum received honorary titles as laureates of the State Youth Award of the Republic of Mari El in the field of literature, culture, and art named after Olyka Ipaya. The award ceremony took place in January 2015 at the House of Government of the Republic of Mari El.

On July 20, 2017, during a visit to Yoshkar-Ola to participate in a meeting of the Council for Interethnic Relations under the President of Russia, the museum was visited by President of Russia V. V. Putin.

In March 2020, to mark the 100th anniversary of the museum, a presentation of new products and services took place at the Museum of History and Archaeology. A presentation album "Mari Land, Charm of Russia" was introduced along with a mobile application "I Am Here: Mari El" for iOS and Android. New opportunities for business participation in the development of culture in the Republic of Mari El and the creation of cultural clusters were discussed. Participants included representatives of companies interested in expanding marketing channels and new approaches to corporate culture.

The museum building is a monument of regional architectural significance.

Built in 1903 as a detention house, it later served as a labor faculty, and during the Great Patriotic War, it housed the State Optical Institute from Leningrad, where academician Sergey Ivanovich Vavilov worked. The museum has occupied the building since 1946. In 1960, for the anniversary of the republic, the building was renovated, adding a third floor and constructing a right wing.

The building forms the front of the eastern side of Sovetskaya Street. It is a rectangular three-story brick structure with a risalit on the eastern side. The facade features rustication, profiled cornices, fluted strips in the window reveals of the 2nd and 3rd floors, and decorations in the form of Mari national ornamentation.