Agistri along with Aegina and the neighboring islands consisted of the Kingdom of Aegina of the mythical King Aeakos.

According to Homer, Agistri was called Kekrifalia, which means "adorned head" and appears as an ally of Aegina during the Trojan War.

Tradition notes that visitors amazed by the natural beauty of the island were caught like fish on the hook and lived there for all their lives (Agistri means fish-hook).

Other historians who mention the island in their papers are Thoucydides and Diodorus.

Kadoudi, Megaritsa and Kodari are of archaeological interest.

Throughout the whole of the island's west coast there are antiquities situated just below the sea surface.

There are various archaeological findings in Megalochori at the Cultural Center.These findings indicate that the island was first inhibited at least starting from the 5th century B.C. by Peloponnesians who came to the island.

In general, concerning the island's history not much has been recorded by historians. At times, in its more recent history, roughly in the 14th century, Agistri received many settlers from the coasts of Peloponnese, situated right across it. Later on, Agistri became a part of the Ottoman Empire.

At the end of the 17th century, the inhabitants left the island, due to frequent raiding by pirates.

In 1821 the island was yet again inhadited by a small number of people. In 1835 the Community of Agistri was formed by Royal Decree. According to the inventory that took place at the time, there were 248 inhabitants. Until 1940 the island's inhabitants remained few.

After 1940, the number started increasing and today it has more than 1.000 inhaditants, which, during the summer reach up to 5.000.

Until 1960 the island became directly connected to Piraeus and in 1973 electricity was supplid to the island.