The Austrian Archaeological Institute was founded in 1898 as a reaction to the extremely successful excavations in Ephesos (since 1895). For many years the OeAI was a subordinate department of the Federal Ministry for Science but on January 1, 2016 it became a research institution of the Austrian Academy of Sciences (ÖAW). Its staff members in the head office Vienna as well as the branches in Athens and Cairo are responsible for numerous archaeological projects within Austria and abroad. The most important research site of the OeAI is Ephesos on the west coast of Turkey.

On October 1, 1898 the imperial-royal Austrian Archaeological Institute in Vienna began its scientific activities. Around one and a half years previously the emperor Franz Josef I had authorized the establishment of the institute with his signature. At the time the OeAI was responsible for uniting all activities of the monarchy within the area of classical archaeology. This included scientific research (especially excavations in Austria and abroad as well as their publication), the administration of the museums in Aquileia, Pula, Zadar, and Split which belonged to Austria at the time, and the awarding of international scholarships.

The foreign posts of the imperial-royal Ministry for Cultus and Teaching in Constantinople/Istanbul, Smyrna/Izmir and Athens were assumed in 1898 by the OeAI. The office in Constantinople was given up in 1901 while the offices in Athens were moved to a separate building. The institute building for the Athens branch was built according to plans by the architect Ernst Ziller on ground given by the Greek State for this purpose located along the Leoforos Alexandras and opened in 1908. From 1947 to 2003 the Austrian Embassy was also located in this building.

The excavations in Ephesos began in 1895 under the direction of the institute and were managed in the beginning by the branch in Smyrna. In Greece the OeAI conducted surveys in Lousoi, Elis, and Aigeira (Peloponnese) – sites that like Ephesos have remained a focus of Austrian archaeological research.

In the economically difficult times following the collapse of the monarchy, the institute managed to remain active, however, the branch in Izmir hat to be abandoned and the number of staff had to be reduced to a minimum. Its survival was only ensured through its inclusion in the University of Vienna (1935). But even in these difficult times numerous research projects were advanced including the uncovering and conservation of the amphitheater II of Carnuntum in the 1920s.

Following the annexation of Austria into the German Reich (1938) the institute lost its independence in 1939 and became a branch of the Archaeological Institute of the German Reich. In 1954 its status of 1935 was reestablished.

The OeAI continued its scientific activities following World War II with very little staff and mainly conducted excavations within Austria. In the 1950s the excavations in Ephesos were resumed, in 1964 the Athens branch was reopened, and in 1973 the Cairo branch was founded.