According to the writings of Yaroslavl historians Athanasian monastery was founded after 1612, at a time when near the Church of Athanasius and Cyril in the chapel has been the finding of the miraculous icon of the Savior. But there is documentary evidence that the monastery existed already in the 16th century In 1615 Gavriil Makushkin, district superintendent, addressed to the Metropolitan of Rostov Cyril to bless the Foundation of the monastery on the sacred place.

There is documentary evidence that the Athanasian monastery was ruled by abbots. In the first years of its existence it has already received tenure and privileges according to charters of Mikhail Fedorovich. In the first letter, dated 1619, it was said that the Athanasian monastery exempt from Ruga money and food, candles, wine, incense. Also the monastery was allocated a place under the mill on the Romanov and the Yaroslavl side. With the forest and the wood that the monastery was carrying on the Volga, the Mologa and Sheksna to the monastery life duty is not levied. The monastery also were relieved from the post of Governor, the boyars, princes and military people.

The first buildings were wooden, in the 17th century the monastery was repeatedly destroyed in the fires. So, in 1658, the monastery was completely destroyed. The first stone Church of the monastery in honor of Athanasius and Cyril was built in 1664 with the blessing of Metropolitan of Rostov Jonah Sysoyevich. Upon completion, the Church was decorated with paintings made by Moscow masters. In the fire of 1670 the monastery again suffered. In 1676 to the Cathedral Church to the North was built winter Church with a bell tower, which was consecrated in honor of Metropolitan Alexis of Moscow. In 1736 at the request of the Abbot of the monastery of Iona, and by decree of the Archbishop Joachim to Afanasievsky monastery attributed the chapel attached to the sign or the exhibition hall of the tower, which was the gateway to the Earthen city. Today it is known as Znamenskaya Church.

Athanasian significant monastery was never in the richness of their possessions, or the number of monks: in 1717, there were only seven monks so one belets; staff has not increased and according to 1802, the monastery was quite small, it was limited to the low stone wall just East and North-East. Other parties as the fence was made by the monastery's outbuildings Philistine houses, as well as the Saviour Probinsya Church.

On the East, the front facade of the monastery, who had a Breakdown on the street, in the 18th century, built two stone towers of small size, one of them played the role of the Holy gates, the other housed a chapel in honor of an important event − the discovery here of the miraculous icon. Towers had spires over with figures of trumpeting angels.

June 25, 1768 in the center of Yaroslavl in ordinary time the fire occurred. In the list of the damage is contained, in fact, the first description of buildings the Athanasian monastery. When restoration work was updated painting of the Church of Athanasius and Cyril, the original stone iconostasis was replaced with wood.

In 1820-1830 in the monastery were carried out large-scale work on its improvement: were built two-storey stone Abbot's rooms and refectory; were arranged two sister cells; for the Church of Athanasius and Cyril in 1825 tradesman Constantine of Service produced at his own expense a new iconostasis, Alexander Chrysikou from Yaroslavl gilded it; in 1831, warm Church was decorated with paintings, murals executed Timothy Medvedev. At the same time it was rebuilt single-tiered bell tower over the porch warm the Church, from the abolished monastery of STS parish was transferred to 115-pounds bell. The ensemble of the monastery bell tower was seven bells.

Another realignment Athanasian the monastery was destroyed at the turn of 19-20 centuries: in 1897 were arranged in a stone cellar, a coach barn, bath, stable; in 1903 and 1907. repair work was carried out in the Cathedral Church, with funding from F. E. Vakhrameev; in 1912, was were renovated, wall painting artist and restorer M. I. Dikarev on donations A. And vahromeeva.

In 1764 by decree of Empress Catherine II Afanasyevsk the monastery was considered to be unimportant. December 12, 1857 Afanasyevskaya the monastery was raised to the third class degree, the abbots had it this time with a dignity of Archimandrite. Since 1895 Athanasian monastery received the status of residence of a vicar Bishop of the diocese of Yaroslavl.

After the revolution, when the Athanasian monastery was established parish community. In February 1925 the monastery was closed, a part of its property was transferred to the Church of the Savior on the City and other temples. In the 1930s, by the decision of the city authorities, the bell tower was demolished, and the Church of Athanasius and Cyril, and other monastic buildings housed the organization, production workshops, fraternal building was used for housing.

In November 2007, the temple with a wall and towers of the Holy gates gave the Russian Orthodox Church. When the Yaroslavl theological Seminary moved to the manor vahromeeva by order of his Eminence Kirill monastery Church became a Seminary. January 31, 2008 in the chapel of Alexius was committed first service.