Since 1973, the Archaeological Collection of Arta has been housed in the refectory (dining room) of the Paregoretissa Monastery, a building of the 13th century. The collection includes funerary stelae and burial offerings from the cemeteries of ancient Ambracia, finds from the ancient city of Ambracia, the "Koudounotrypa" cave, and several other sites in the region of Arta.

However, the huge volume of mobile artefacts from the rescue excavations of the last decades of the 20th century made it imperative to establish an Archaeological Museum in the city, both for the presentation and exhibiting the most important of these, as well as for the safe storage of the rest.

The effort to establish the Museum, which began in 1979 and continued in 1994 with the relevant approval decision by the Ministry of Culture, led in 1995 to the final selection of the location in the "Trigono" area, next to the bank of the Arachthos River and a short distance from the historic Bridge of Arta, after the Municipality of Arta granted a 9,800 m² plot of land to the Ministry of Culture.

The project of constructing the Museum was included in 1999 in the Regional Operational Program of the Third Community Support Framework, with the Region of Epirus as the implementing body, and was completed in the fall of 2006, when it was administratively taken over by the L.G. Ephorate of Prehistoric and Classic Antiquities. The building, with a total area of 1,549 square meters, includes 500 square meters of exhibition space around the central atrium, two conservation workshops, spacious storage rooms for finds, administrative offices, multipurpose and educational program rooms, as well as public service areas, such as a cloakroom, a shop, and a refreshment area.

The project for the exhibition and equipment of the Museum, with a budget of €1,800,000, began in June 2006 with funding from the Regional Operational Program of the Third Community Support Framework and implemented by the L.G.E.P.K.A. The project provided the necessary material and technical infrastructure for the operation of the conservation workshops, storage areas, offices, and public service areas.