The oldest temple in Novgorod and one of the first in Rus, dedicated to the holy martyrs Boris and Gleb, was founded in 1146 on the site where a wooden Sofia temple with 13 domes previously stood. In 1167, the wooden church was replaced with a stone one, which was consecrated in 1171.

Chronicles mention that the temple was "magnificent and beautiful." It has repeatedly burned, been destroyed, and rebuilt. In 1405, a fire completely destroyed it, and in 1411, Archbishop Euphymius erected a new church of Boris and Gleb on the old foundation. The temple was finally dismantled in the second half of the 17th century, and in its place in the Kremlin now stands the Church of Andrew the General.

To this day, only the Church of Boris and Gleb in Plotniki has survived. Its history is known from chronicles, descriptions of Novgorod antiquities by Archimandrite Macarius, and modern research. The first mention of the stone single-domed church of Boris and Gleb dates back to 1377. The church suffered from fires multiple times and was ultimately dismantled due to dilapidation.

In 1536, the construction of a new stone five-domed church with two chapels dedicated to St. Nicholas the Wonderworker and St. Vladimir began. Residents of two streets, Zapolskaya and Konyukhova, as well as guests from Moscow and Novgorod participated in the construction. The church was erected in five months and consecrated in 1537. Thirty people participated in the construction, of which twenty were masters. In the 16th century, the church was considered a cathedral, and in the 17th century, a parish church. On the day of Boris and Gleb in the 17th century, an archbishop's service was held in the church.

The cathedral has preserved its original architectural forms and represents a four-pillar cubic structure with a semicircular apse and a lowered western narthex, topped with five domes. The facades are divided by pilasters into three sections. The architectural solution is typical for Novgorod architecture of the republican period. The five domes, the arrangement of the undercroft, the multi-gabled completion of the facades, and the friezes of pentagonal niches all reflect new trends in architecture. The Church of Boris and Gleb is two-storied with one altar apse and an annex on the western side. In the 18th century, the southern chapel of St. Nicholas the Wonderworker was moved to the western narthex, and the chapel of St. Vladimir to the underchurch. It was also during this time that the Pokrovsky chapel in the northern part of the narthex was first mentioned. Some icons from the church's iconostasis have survived and are now in the Novgorod Museum.

By the beginning of the 20th century, the church fell into disrepair and was considered one of the poorest in the empire. After 1907, it was repaired, and architect V. V. Suslov made the first measurements of the 16th-century temple. In April 1933, the church was closed. In the 1950s, restoration work was carried out under the guidance of Z. I. Vasilieva, and in the 1960s and 1980s, research and restoration continued with T. V. Gladensko and V. A. Popov. In 1992, the church was transferred to the Novgorod diocese and consecrated on August 6 of the same year.