The foundation of the church is linked to the construction of the Vologda Kremlin at the initiative of Ivan the Terrible. In the "Vologda Chronicle," Ivan Slobodskoy mentions that in 1566, the tsar ordered the laying of a stone city on April 28, the feast day of the holy apostles Jason and Sosipater. Historian N.I. Suvorov associates this date with the construction of a wooden church in their honor, which became the predecessor of the Kazan temple. The church was located near the royal palace, and the palace's domestic church was the church of Joachim and Anna, later consecrated as the Protection Church.

The toponym "na Torgu" appeared in the 20th century due to the proximity of the market. The trading rows were located near the Kazan church since the 17th century. In the 17th century, the church was referred to as "near the Fish Row," and later "on the Swamp," which is related to the marshy terrain.

In 1605, the churches of Joachim and Anna, Jason and Sosipater, as well as the royal palace, burned down in a fire.

In 1760, the current stone church was built. In the 18th century, it was painted, presumably by the artists of the Spaso-Prilutsky Monastery, Yakov Alekseev Korostin and his son Fyodor. Later, the paintings were updated. In 1820, the Kazan church was annexed to the Protection Church on Torgu. In 1832, it was converted into a warm church for winter services, while summer services were held in the Protection Church. From this time, the parish is called the Protection-Kazan parish. On May 14, 1907, John of Kronstadt celebrated the Divine Liturgy in the church on his way to his native village of Sura. This was his last visit to Vologda.

On June 4, 1929, the church was closed. In the same month, two organizations submitted requests for the transfer of the building: the workers' cooperative "Vologzhanin" for confectionery production and the Selkredsoyuz for a tractor repair workshop. However, the authorities decided to use the premises for storing documents of the Okrarchivbureau. In the 1930s, the church lost its completion, and in the late 1940s and early 1950s, the tented bell tower was dismantled, partially damaging the refectory. Until the 1970s, the building housed trading offices for selling dairy products. After the relocation of the city market, there was a proposal to build a high-rise administrative building on Torgovaya Square and demolish the church. However, the authorities abandoned these plans and built a new regional executive committee building on Herzen Street, now the regional government building.

The restoration of the church began in the early 1990s under the guidance of the rector of the Protection Church on Torgu, Archpriest Vasily Pavlov, and the community led by D.N. Tikhomirova. The revival of the Protection-Kazan parish began. In 1992, the dilapidated building of the Kazan church, without a bell tower and domes, was handed over to the Protection community. On February 20, 1995, by decree of the President of the Russian Federation, the Kazan temple was recognized as a cultural heritage site of federal significance. In the 2000s, the restoration of the church began according to the project of architect G.P. Belov: the domes and damaged sections of the masonry were restored, and the restoration of the bell tower was initiated. On June 16, 2014, a separate parish was formed around the church. On July 20, 2014, the first service was held in the church, a moleben before the Kazan Icon of the Mother of God. On May 11, 2015, Metropolitan Ignatius of Vologda and Kirillov celebrated the first Divine Liturgy in 86 years. In September 2017, the installation of the iconostasis in the chapel of the holy apostles Jason and Sosipater was completed. Restoration work continues in the church.