The new synagogue was built in the middle of the 19th century. It was built by the town’s richest tailor I. Vilneris. It is a two-story building. Men would pray on the first floor and women on the second floor. Two memorial tables in Lithuanian and Hebrew were placed on the wall of this synagogue in memory of the great Jewish religious thinker Gaon Elijahu of Vilnius. The old Kedainiai synagogue stands at the same place.
Since 2002, a multicultural centre has been operating in the synagogue with an exposition on the community of Kėdainiai Jews and the Holocaust. Many cultural events, music concerts as well as exhibitions and seminars are held in the centre.