After the baptism of Rus, churches began to be built on its territory, predominantly wooden, which often fell victim to fires. In their place, thanks to the efforts of princes, stone temples emerged. One of these was the Novgorod cathedral in the name of Sophia, the Wisdom of God. In 1045, a fire occurred in Veliky Novgorod, destroying the wooden Sophia church, built at the end of the 10th century shortly after the baptism of the local population. The church was made of oak and had thirteen domes; it was located outside the kremlin. After the fire, Novgorod prince Vladimir Yaroslavich laid the foundation for a new stone cathedral in the detinets. His parents, Grand Prince Yaroslav the Wise and Grand Princess Irina, who later took the veil under the name Anna and was canonized as Saint Anna of Novgorod, were present at the laying.

Traditionally, the construction of the cathedral is associated with Prince Vladimir Yaroslavich's victory over Byzantium in 1044, although the chronicles do not contain information about this campaign. Only Vladimir's campaign to Constantinople in 1043 is known, which ended in defeat for the Russian troops. The Russians were met with 'Greek fire' at the city's walls, and a storm completed their rout. The Russians retreated, and the captured were blinded by the Byzantines. Perhaps after this unsuccessful battle, Vladimir wanted to take revenge. Although no reliable sources about the campaign to Constantinople in 1044 have been found, relations between Rus and Byzantium improved after that year. Emperor Monomach married his daughter Anastasia to Vsevolod, son of Yaroslav, symbolizing reconciliation. Some researchers believe that from the 1044 campaign, Vladimir could have brought icons related to the early Novgorod school. The stone cathedral was built under the supervision of the prince and Bishop Luka Zhidyata and was completed in five years.

In 1929, the Sophia Cathedral was closed and transformed into a museum, opening all its premises to visitors. In 1991, the cathedral was handed over to the Church after thorough preparations. Restoration was carried out, and a Consultative Council was created to preserve the monument. On August 16, Patriarch Alexy II consecrated the cathedral, the first liturgy took place, and during the procession, a rainbow halo appeared over the temple.

The situation of the Sophia Cathedral is unique. The ancient temple, included in the UNESCO World Heritage List, has been handed over to the Church, which is responsible for its preservation.