Most of Valkininkai's Jewish properties were concentrated near the market square and in the surrounding streets. In the second half of the 18th century, a large wooden synagogue of original architecture was built here, which became an important highlight of Valkininkai and emphasized the location of the city center. Valkininkai Synagogue is one of the most famous and significant synagogues with original wooden ornamental architecture in Lithuania. The founder of the synagogue was nobleman Granovskis, who supplied the lumber. Like all wooden synagogues of that time, Valkininkai Synagogue was built on hewn foundations made of stone and bricks and covered with a high, multi-tiered roof made of shingles. A second synagogue was built before 1880.
According to the old residents of Valkinkai, this prayer house was always open and anyone
could enter it whenever they wanted. The synagogue was almost always closed and was only opened during major religious holidays. In the late 19th century, there was also a Jewish school in Valkininkai. In 1912, a primary school was opened. According to older residents, between 1936 and 1938, in addition to the Polish school with its 7th grades, there was also a Jewish school in Valkininkai.
In 1941, it was destroyed a few days after the German Wehrmacht invaded.