The first chapel on the territory of the military hospital was built in 1825, shortly after the hospital was relocated beyond the Omsk fortress to the Butyrsky fort on the right bank of the Om River. It was a wooden building with an octagonal base and a small dome, attached to the now-destroyed Resurrection Cathedral. In 1854, the chapel was transformed into an independent church.

However, by 1857, the wooden structure was dismantled due to its dilapidation. This chapel entered the history of Omsk as the place where F.M. Dostoevsky prayed.

Since 1899, various architects proposed designs for a new church, but none satisfied the local administration or the clergy. Architect A.I. von Hohen initially suggested a wooden church design, but priest Father Alexey Serebrennikov insisted on a stone building. The final project was approved in January 1903. A.I. von Hohen, inspired by Russian architectural traditions of the 17th century, created a design in this style. The church had an elongated shape with two chapels and one apse in the altar part. The chapels were adorned with multilayered friezes, cornices, and arches, windows with keel-shaped decor and broken pediments. The facades were decorated in the traditions of Russian architecture: rusticated corners, balusters and pilasters, half-columns, 'dry loaves', and niches in the plinth. The bell tower had an octagonal shape with carved arches and a tent roof. Inside, the space was divided by vestibules, and the walls were painted with oil paints. The estimated cost of the church was 33 thousand rubles, and construction was funded by donations from the townspeople. Contractors changed several times, but in December 1906, the building was consecrated. A year later, a chapel of Seraphim of Sarov and Saint Alexius was built near the bridge over the Om River, attached to the church.

In 1921, the church was closed and used as a storage facility for the military hospital. The domes and bell tower were dismantled. Restoration began in May 1989 when the building was recognized as an architectural monument and entered into the register of protected objects. Soon, the church was returned to the Russian Orthodox Church. Today, the building is fully restored and regular services are held there. However, access to the church is only through a checkpoint, as it is a military hospital. Guards allow entry upon presentation of identification and accompany visitors on the hospital grounds.