Originally, this was the southern corner tower of the monastery, where a church was established in 1763. This occurred under the Astrakhan bishop Mephodius, and the church was consecrated in honor of St. Hilarion the Great. The work on the church was financed by the bishop in memory of his uncle, Bishop Hilarion, who had previously held the position of Astrakhan archbishop. In the same 1760s, Bishop Mephodius established another church in the northeastern tower in honor of St. Mephodius, Patriarch of Constantinople, the heavenly patron of the bishop. Currently, the Catherine Church is located on this site.

By the mid-19th century, the church fell into disrepair, and the monastery lacked funds for its restoration. Astrakhan merchant Joakim Andreyevich Repin offered to restore the church at his own expense, on the condition that the church would be renamed in honor of St. Barbara the Great Martyr in memory of his deceased wife, and that a family crypt for the Repin family would be arranged under the church. Astrakhan Archbishop Athanasius Drozdov agreed to these terms, allowing the renaming and the arrangement of the crypt. In 1867, the church was repaired and reconsecrated as the Barbara Church. A new iconostasis was created with the funds from merchant Repin, and the church was adorned with sacred images.

In 1893, a fire occurred in the southern cells, damaging the Barbara Church, especially its iconostasis. Repairs were carried out with donations from the same merchant Repin.

During the Soviet era, the church's decor was lost. By the early 20th century, the former church was used for the needs of a hospital, and here, as well as in the southern wing of the brotherly cells, there were hospital wards. Currently, restoration of the church has begun.

The small warm church is executed in the style of "Naryshkin" Baroque. Its main decoration, the altar, was rebuilt from the corner tower with a tent roof. The church did not have a refectory and was directly connected to the southern wing of the brotherly cells. Under the church was a crypt for the Repin family.