Jews likely settled in Veisiejai in the early 18th century and the documentary evidence, in the form of a building permit dating to c.1748, suggests that a synagogue was first built around that time. In 1799 a new wooden synagogue was built but a little under a 100 years later in 1872, it was destroyed by fire. A subsequent replacement built a year later also burnt down but was restored on a number of occasions between 1882 and 1924.
The former Beit Midrash building that stands today is of early 20th century construction and it would have originally comprised of a prayer hall on the east side and on the west side, a group of rooms and a first floor women’s section. Today, the building serves as a Baptist church.