Construction of the museum began in 2007 with funding from the Japan International Cooperation Agency and the Japanese government.

[3] In 2021, a virtual museum exhibition funded by the Science and Technology Foundation and implemented by the National University of Mongolia was organized for the 800th anniversary of the founding of Kharkhorum.

In 2020, it was recorded that the museum contained 3128 artifacts, some of these dating from the Upper Paleolithic period to the 14th century.

In addition, the museum contains seal with phags-pa script, this script is an ancient Mongolian writing method, it is considered as a very important artifact of this seal was used by a finance minister of the emperor of Northern Yuan dynasty Biligtü Khan Ayushiridara.

The museum contains 300 Mongolian imperial coins with inscriptions in arabic and phags-pa script, found in Karakorum during 2000 to 2005.