The Intercession Church was built outside the fortress, near its northern wall. The temple was erected by Cossacks living in a small settlement and on a farm on the northwestern side by the Lopan River. In 1724, the parish had only 87 parishioners with families. The names of the founders are unknown, but the church was built by masters familiar with folk architecture, Ukrainian baroque, and Moscow architecture. In composition, it resembles typical three-log wooden churches of Ukraine with a separate bell tower, but it has two floors. At the base of the temple is a basement surrounded by an arcade. In the basement is a single-altar winter church in the name of the Three Holy Hierarchs. On the upper floor, surrounded by a gallery, is a single-altar summer church in the name of the Intercession of the Holy Virgin, originally unheated. A burial vault for local nobility was later arranged in the basement. The central octagonal volume is connected on the west side to a hexagonal altar part and on the east side to a similar narthex. The octagonal tower volumes of the upper church are divided by tiers and topped with domes with crosses. The height of the church in the central part is 48 m. The outer walls are decorated with cornices with a toothed parapet, and the corners are accentuated by half-columns on brackets. The window openings are framed with moldings with columns and ornate lintels. Inside the upper church, the bright space of three chambers connected by arched openings creates a beautiful effect. The bell tower, built simultaneously with the church, was connected to it by a gallery. It is octagonal, four-tiered, with a basement, resembling a defensive tower. It is topped with a ringing tier, above which rises a stone tent with windows and a small dome with a cross.

In 1709, by the order of Peter I, who visited Kharkiv, the fortress was expanded to the north, and the Intercession Church found itself within its territory. The land around the church belonged to Colonel Fyodor Shidlovsky. The site had wooden buildings and the construction of a stone house had begun. In 1708, the ownership passed to Lavrenty Shidlovsky, Fyodor's nephew, and the plot with the garden and buildings was given to Prince Kantemir.

In 1726, an important event in the cultural life of Slobozhanshchyna occurred, affecting the fate of the Intercession Church. In Kharkiv, at the initiative of Bishop Epiphanius Tikhorsky and Prince M.M. Golitsyn, the Holy Intercession Men's School Monastery with a Collegium was founded, the first higher educational institution in the Left Bank. From 1729, the church became monastic and collegial. It was repaired, decorated, and supplied with church utensils. In 1732, a bell weighing 1.6 tons was installed in the bell tower. In 1799-1800, the upper church was transformed into a cathedral, while the lower one continued to serve the collegium. The sacristy housed many church relics, Gospels, crosses, candlesticks, and more. In the burial vault, clergymen and prominent citizens were buried.

From 1820 to 1826, during the construction of a new Archiepiscopal residence, a passage and refectory were built between it and the church, uniting the church with the bell tower. In 1837, the domes and crosses were gilded. In 1846, the Assumption Church again became the cathedral, to which a bell tower was added, while the Intercession Church became the main cross church of the Archiepiscopal residence. From 1844 to 1856, it was painted and heated with hot air. In 1872-1874, the refectory was expanded, the staircase to the second floor was rebuilt, and choirs were arranged.

In the 19th and early 20th centuries, work was carried out in the monastery to build new buildings and improve the territory. The Ozyeryanska Church, a basilica building next to the Intercession Cathedral, the rector's house with the main gates, the former Consistory, a building of cells with a refectory and an apartment for high-ranking clergy, a chapel with spare gates, and several residential and service buildings were erected.

In the early 1920s, the Holy Intercession Monastery was closed. Museums and organizations were placed in its buildings. The Intercession Church was used haphazardly and fell into disrepair. The first attempt at restoration was made in the 1950s; it was cosmetic in nature but saved the temple from destruction. In the 1960s, it was decided to restore the church to its 17th-century appearance, dismantling parts added in the 19th century: the refectory and passages to the Archiepiscopal residence and Ozyeryanska Church.

In 1992, the complex of the Holy Intercession Monastery was returned to the church. The buildings and architectural monuments on its territory were transferred to it. By agreement with the Diocesan Administration, the premises will be used by organizations and for the apartments of residents. Restoration work on the Intercession Church continues, with services resumed in the lower church. The new restoration project includes the reconstruction of previously dismantled parts.