As a result of archaeological excavations that began in Bergama in 1878 under the direction of Carl Humman and Alexander Conze ; a storehouse was built near the German Excavation House during the excavations made in the acropolis between the years 1900-1913 . This store is one of two archaeological depots in Türkiye at that time. Excavations in Bergama, which were interrupted due to World War One, were resumed in 1927 under the direction of Theodor Wiegand. In addition to the acropolis excavations in the same year, the excavations started in Asklepion and a new museum building was needed.
Marshal Fevzi Cakmak, who came to Pergamum in 1932, was interested in the subject and ordered to establish a new museum after his visit. The present site, which is an old cemetery, was considered suitable for the new structure planned to be realized by Türkiye-German cooperation.
The project, which was planned by the architects Bruno Meyer and Harold Hanson, was finished at the end of 1932. The excavation works were started in 1933 by the request of the Izmir Governor Kazım Dirik. During his visit to Bergama on April 13, 1934, Mustafa Kemal Atatürk also visited Asklepion, a health center, and saw that the museum building was still under construction.
The Pergamon Museum, whose construction was completed, was opened on 30 October 1936 by İzmir Governor Fazlı Güleç. The museum building consisted of a rectangular courtyard surrounded by large and surrounded by galleries, and a rectangular exhibition hall behind this courtyard. Since the galleries of the courtyard were suitable for the open-air museum, the artifacts were exhibited here.
In 1924, when the Ethnography and Archeology Museum was opened in Bergama People's House building, the archaeological artifacts were moved to the new museum building. Ethnographic artifacts were included in the museum building in 1979, after the construction of the additional building. The additional building is located in a rectangular plan, which is situated transversely to the side of the courtyard and the exhibition hall, and its entrance is provided by a door opening from the courtyard to the hall. On the other side of the museum, which was left blank, units such as warehouses, laboratories, photographers and archives were added to the back.
Most of the archaeological artifacts from the Early Bronze Age to the Byzantine Period were excavated in Bergama and its environments .  
Among the finds from the ancient settlements in the vicinity, examples from the Pergamon sculpture school, the Archaic Period finds from Pitane and Gryneion, and Myrina terracotta are noteworthy. In the ethnography section, carpets, rugs (Yuntdağ, Yağcıbedir, Kozak Bergama weavings), fabric weaving samples, hand embroidery and hand-made artifacts belonging to other regions of Anatolia are exhibited in the ethnography section.