In the year 1902, a museum was constructed on the north of Ananda Temple by Mr.Taw Sein Kho. He was the Superintendent of the former Epigraphic Office / Department of Archaeology of National Museum and Library. The museum was eventually opened for public in the year 1904. This small museum was characterized by unsystematic displays.
In 1979, towards the south of Gawdawpalin Temple within old Bagan, a modern museum was constructed. This complex of buildings and octagonal looking structure displayed ancient objects. There were three sheds that depicted stone inscriptions & sculptures, and various large size archaeological finds.
By early 1995, it is believed that the three sheds were razed but octagonal structure was not demolished. Eventually a new museum was built near the old museum and its inauguration was held in the year 1998. It was erected on a land of 10.97 acres.
The museum has ten exhibition rooms. There are special display rooms and galleries in the museum that are dedicated to various themes such as Bagan Arts and crafts, Bagan Palace city, Buddhist art of Bagan, Buddha images of Bagan, Bagan period literature, Bagan period social life, Bagan period Architecture, Bagan period Frescos (Mural paintings), paintings presenting Pagodas and monuments of the Bagan period.