The first Jews came to the town in the 17th century, but, for nearly 200 years, they constituted only a minor percentage of its inhabitants. There was a breakthrough when the monk Wawrzyniec Bordkiewicz became the procurator of the convent in Sejny [1.1]. In order to bring financial capital into the town, he decided to draw a higher number of Jews to Sejny. For this reason, he ordered to erect a wooden synagogue in 1788. The legend says that, during the celebration of its opening, the prior himself [and perhaps the procurator of the convent – vide the note above] brought a Torah scroll into the synagogue, whilst, as Aleksander Połujański, the author of descriptions of the surrounding area reported, the Jews from Sejny used to pray in the synagogue for their benefactor Bordkiewicz as late as in 1859 [1.2].

From the end of the 18th century, the number of Jewish inhabitants began to increase, which resulted in a resulted in a fall of the nearby Krasnopol. In mid-19th century, Jews constituted  72% of the total number of inhabitants of the town. A yeshiva was set up on the initiative of Mojżesz Icchak Awigdor, whilst, in the years 1860–1870, a new masonry synagogue was erected. At that time, the famous rabbi, Mojżesz Becalel Luria, was active in the town and Sejny became an important Haskalah centre among Lithuanian Jews.

In the years 1870–1900, the town experienced a serious crisis and the Sejny Jews were overwhelmed with poverty. Due to its peripheral location and a lack of a railway line, no large industrial plants were established in the town.

In the 20th century, Zionism was very popular in Sejny. On the initiative of Tuwi Pinkas Szapiro, the Hebrew gymnasium was set up in the town.

In 1939, Sejny was under the German occupation. In October 1939, the Germans gathered all Jews and transported to the no-man's land between the occupied territories and Lithuania. Some of the Jews returned, but most of them moved to the Lithuanian side.