In the first half of the 19th century, the Peski area on the northern outskirts of Kharkiv was a small settlement of 30 houses made of wood and clay, with thatched roofs. The residents, mostly Ukrainians, engaged in agriculture and trade, transporting goods between the south and north before the railway was built. Peski bordered University Hill and a garden to the east, the Bedryagin lands to the west, the Serdyukov lands to the north, and swamps to the south, which later became a cattle yard. Over time, Peski began to be rapidly developed, and peasants moved to other places. The only undeveloped plot of land, measuring 784 square fathoms, was left for a university building, where the Panteleimon Church now stands. A source of healing water opened at this site, and by the order of Governor Kokoshkin, wells were dug for the residents.

With the population growth, there arose a need to establish Peski as a separate parish. In 1866, H.G. Fedorov attempted to obtain land for the construction of a church, but due to lack of funds and other reasons, he was unsuccessful. The railway undermined trade, and the governor's ban on storing bread and hay worsened the situation. In the early 1880s, influential residents such as K.N. Zakhariev and N.A. Zheverzhev appeared in the area. In January 1882, a petition was submitted to Bishop Justin, who granted permission for the church's construction. The residents raised 10,000 rubles for the building.

On May 24, 1882, Bishop Justin approved the church plan and appointed a building committee. On June 6, he consecrated the site for the church's foundation. The committee decided to expand the project by adding two altars. The widow of merchant E.M. Ognienko took on the arrangement of one of the chapels. Construction progressed quickly, and by 1883, the walls were erected, and the church was covered with iron. The bell tower was transformed into a three-tiered structure. The interior included icons painted by artist M.F. Plotnikov and donations from local residents.

Architect F.I. Danilov developed the project in the Russian-Byzantine style. In 1897-1898, architect M.I. Lovtsov reconstructed the church, adding decorative elements. After the 1917 revolution, the church was closed and used as a club and school. During World War II, services resumed, but in 1961, the church was closed again. In 1982, the building was handed over to a sports society, but no repairs were made.

In 1989, the church was returned to the Kharkiv Diocese. Metropolitan Nikodim held the first liturgy in the semi-destroyed church. Priest Leontiy Tanashkin became the rector and began restoration. In 1990, the bells were consecrated, and in 1991, the main altar. In 1992, the lost spring was found, and the area around it was improved. In 1995, rector Leontiy Tanashkin tragically died.

On May 26, 1995, Protopriest Nikolai Ternovetsky became the rector. The restoration of the church continued, and by 1999, all work was completed. In 2000, the house of the first rector was returned to the church, restored, and became part of the architectural ensemble.