The Torah ark once occupied the center of the southeastern wall. Its three-tiered wooden construction was carved and painted by an anonymous Jewish craftsman (Lemchenas, “Pakruojo medinė sinagoga,” p. 101). Four steps flanked by panelled hand rails led from the floor to the landing in front of the ark. On the first tier, two composite columns were carved with wine scrolls and separated by imitation marble panels that stood on either side of the ark. The columns supported an entablature, which was inscribed with the verse:

"כי מציון תצא תורה"

(for out of Zion shall go forth the law, Is. 2:3).

On the second tier, two sculpted rampant griffons held the Tablets of the Law in front of four corinthian columns, surmounted by hands raised in priestly blessing. The entablature of this tier is inscribed:

"אתכם על כנפי נשרים ואבא אתכם אלי"

([I bare] you on eagles’ wings, and brought you unto myself, Ex. 19:4).

On the third tier, the Doric aedicula, spanned with a Baroque pediment, included the Russian two-headed imperial eagle with its insignia: sceptre, orb, and crowns. Another, larger crown was attached to the pediment above the eagle. A second double-headed eagle inscribed with the Tetragrammaton was painted above the sculpted eagle. Two lions standing on their hind legs held a crown above the painted eagle. 

The ark was flanked with delicate carved decoration. The top tier of the ark occupied a niche cut into the vault of the ceiling.