The new Pazerai church was designed in 1936 by Stasys Kudokas. The building was supposed to replace the old wooden church standing nearby, where it was becoming increasingly difficult to fit all perishers.

The different parts of the church's volumes rise steadily towards the central dome which is divided by windows on the side. Above the main entrance, a semi-circular arch is well above the main importance of the church, uniting the towers on the sides into one, thus becoming one of the unique towers of Lithuanian churches. The Greek cross-plan interior space is extremely bright: it is illuminated not only by the drum windows but also by the massive narrow vertical windows on the sides.

The new Pazerai church was not finished before the Soviet occupation: the building remained unfurnished. During the Soviet era, the church was nationalized and functioned as a grain warehouse. Believers recovered the church only after the restoration of independence, which was opened in 1997.