The Church of Andrew the Stratilates was built no earlier than the late 17th or early 18th century on the site of the destroyed Boris and Gleb Church, erected in 1167 by the boyar Sotko Sytynich. In 1969, a well-preserved staircase tower of the Boris and Gleb Church was discovered inside the church, which led to the loft and choir.

Originally, a stone temple of Boris and Gleb was built on this site between 1167 and 1173, representing a majestic building with three apses and six pillars, as well as a staircase tower. After a fire in 1405 that severely damaged the church, a new temple was built on the old foundation in 1441 by order of Archbishop Euphemius II. The staircase tower was dismantled, and a chapel of Andrew the Stratilates appeared in its place. The reconstructed Boris and Gleb Cathedral from the 15th century is depicted in the icon "The Vision of the Sacristan Tarasiy" from the late 16th century, adorned with frescoes and two domes, one of which symbolized the chapel of Andrew the Stratilates. On the Swedish plan of 1611, the chapel of Andrew the Stratilates is clearly visible from the southern side of the main single-domed building.

During the capture of Novgorod by the Swedes in the early 17th century, the cathedral suffered greatly. In 1682, the Boris and Gleb Cathedral collapsed and was dismantled, while the chapel of Andrew the Stratilates was expanded and turned into an independent church. The modern building is the result of two main construction periods. The walls of the western volume and the northern wall of the eastern annex from the 15th century are made of Volhov limestone, shell rock, and brick. The architecture of the western portal with an arched finish and decorative eyebrow is characteristic of Novgorod architecture of the 15th century. The eastern and part of the southern wall, as well as the vaults, were built of brick in the 17th century. In the first half of the 19th century, the temple was reconstructed: a new vault was arranged in the western volume, the roof was replaced, a small dome and bell tower were added, and the foundations under the northern wall were strengthened.

During the Great Patriotic War, the church was damaged: the roof was harmed, plaster fell off, and the floors were dismantled. In 1947, the building was repaired. In 1969, under the guidance of Professor M.K. Karger, the foundations of the 12th-century staircase tower were investigated, revealing a well-preserved masonry of the central pillar with a spiral staircase.

In the 1970s, the condition of the monument deteriorated, and cracks appeared in the walls. Under the guidance of architect G.M. Shtender, emergency works were carried out. In 2000-2003, the firm "Desna" conducted restoration based on the projects of O.N. Kovalenko and L.G. Markova. The load-bearing structures of the building were reinforced, and the floor in the western volume was laid with limestone slabs to emphasize the shape of the base of the staircase tower. Under the guidance of E.I. Seregina, artists and restorers from Moscow uncovered and strengthened the wall paintings of the 16th-17th centuries inside the church.