Armenians have lived in Estonia ever since the 19th century, but the community began to form mainly in the 20th century. The first Armenians to go to Estonia were students from the University of Dorpat (now known as Tartu). In the 19th century and until 1918 many Armenians, including prominent Armenian writer, pedagogue, and founder of Eastern Armenian, Khachatur Abovyan, were educated at the university. The Armenian Students' Association "Armenia" operated at the university.

There are currently about 1,500 Armenians living in Estonia, and there are about a dozen Armenian organizations in the country, including Sunday schools in addition to song and dance groups.

Armenians mainly live in cities of Tallinn and Tartu with several families based in Narva and Pyarni.

Armenians are considered a national minority in Estonia. There are a large number of intellectuals among the Estonian-Armenian community.

In 2010, several organizations merged to form the Armenian National Union.

The Estonian religious community of the Armenian Apostolic Church (St. Gregory's) was officially registered in 1993. It joined the Council of Churches of Estonia in November of that year in Tallinn.

In 1994, the Council of the Evangelical Church of Estonia handed over the building of Iani Angelanots to the Armenian community of Estonia for 99 years. After the reconstruction efforts which were funded by Estonian-Armenian benefactors in the year 2000, it now functions as an Armenian Apostolic Church known as St. Gregory the Illuminator.