The late Sheikh Zayed bin Sultan Al Nahyan selected the fort in Al Ain (built in the late 19th century) to be the headquarters of the museum due to the diverse archaeological sites around this city, dating back 5,000 years. Its restoration in 1969 was done with the same local materials with which the fort was built. The Sheikh also ordered the construction of a new building that contained only two halls and was inaugurated in 1971. Two halls were then added in 1975 to accommodate the large number of antiquities that had been discovered in Al Ain.
Under the supervision of the Department of Culture and Tourism of Abu Dhabi, the restoration of the fort and renovation of the museum have been promoted with the aim of increasing the cultural position of this ancient historical building, preserving archaeological collections and using the latest technologies to improve the way they are displayed.