There is first mention of a wooden synagogue in Žeižmariai in the early 18th century but it is probable that a Jewish community had been settled there since the 16th century. Synagogues are further mentioned in both the late 19th century and the early 20th century when fire destroyed much of the town.
Although built in the Romantic style, Žeižmariai is of a more complex plan than the Alanta synagogue. It is of log construction set on masonry foundations and has an elongated rectangular plan. It has a closed annex housing the staircase to the women’s section on the southwest corner. Unlike Alanta, the prayer hall has four columns in its middle section. The fenestration is mixed with high semi-circular arched windows to the prayer hall and rectangular windows on the two-storey part of the building that incorporates the first floor women’s gallery.
The former Beit Midrash has previously been selected as a part of the European Route of Jewish Heritage by the Council of Europe and is currently the subject of a proposed conservation project. In the absence of a Jewish community in Žeižmariai, it is likely that the building will function in an educational and cultural heritage capacity.