During the execution of the city’s first city plan by Kleanthis and Schaubert, there was a provision for the expropriation of the entire area north of the Acropolis as well as for its systematic excavation. Some work started in 1851, from the Archaeological Company in Athens, which remained active, performing sporadic works, until 1912. During the first year of the works, the later roman wall was revealed, while from 1858 until 1912, Greek archaeologists conducted works in the area of the late roman palace of the “Stoa of the Giants”. In the time between 1859 and 1862, the Stoa of Attalos was brought to light. The works continued from 1898 until 1902. 

Many antiquities were found during the excavations for the railroad lines which connected Athens and Pireaus from 1890 until 1891: the most important constructions which were revealed in part or in whole at that time were the altar of the 12 Gods and some minor sanctums. There was also a research by the German Archaeological Institute from 1891 until 1898 which yielded many results, as a series of monuments in the western part of the Agora (temple of Apollo Patroos, of Zeus Fratrios and Athena Fratria, Metroon [Registry] and Old Bouleuterion). There was also a partial research of the inside of the temple of Hephaestus, the so-called Theseion.  

The Hellenic state, at the risk of having the area flooded with refugees after 1922, tried to appropriate the area anew and conduct research, but this was not possible due to the lack of resources.

In 1925, the Hellenic State turned to the foreign Archaeological Schools which resided in Athens, asking them to undertake the tremendous work of excavations in the area of the classical Agora. The American School of Classical Studies responded to this call and it has been conducting systematic excavations in that area from 1931 until today. In order for the entire area to be revealed, about 400 new buildings in an area of about 120,000 square meters had to be demolished. 

The period between 1931 and 1940 marks a revolution in classical archaeology as well as in the way in which the American classical archaeologists handled research. The works ended during the war but began anew in 1947. Since 1980, the area across the Agora is also included in the excavation. The research in that location has revealed the altar of Aphrodite Urania (daughter of Heaven) and the Painted Stoa (Stoa Poikile). The excavations are ongoing until today. 

Apart from the excavation works, also important are the restoration works that took place in the Agora. The most important achievement was the restoration of the Byzantine temple of Agioi Apostoloi (Holy Apostles) and the reconstruction of the Stoa of Attalos, in 1957 (using mostly modern materials).