According to the writings of historians Afanasievskiy Yaroslavl Monastery was founded after 1612, at a time when next to the Church of Athanasius and Cyril was in the chapel of the acquisition of the miraculous icon of Our Saviour. But there is documentary evidence that the monastery already existed in the 16th century. In 1615, Gabriel Myakushkin, a district mayor, asked the Metropolitan of Rostov Kirill to bless the foundation of the monastery in the holy place.

There is documentary evidence that the Athanasian monastery abbots ruled. In the first years of its existence, it has already got possession of charters and privileges of Mikhail Fedorovich. The first literacy, dating from 1619, said that the Athanasian Monastery exempt from rugi money and bread, the candles, the wine, on its last legs. Also, the monastery was allocated a place in the mill on the side of the Romanov and Yaroslavl. With wood and wood, which was carrying a monastery on the Volga, Mologa and Sheksna related to the monastic duties will be charged. The monastery also exempt from billeting governor, nobles, princes and military men.

The first buildings of the monastery were wooden, in the 17th century. abode repeatedly burned during the fires. For example, in 1658 the monastery was burned to the ground. The first stone church of the monastery in honor of Athanasius and Cyril was built in 1664 with the blessing of Metropolitan Jonah of Rostov Sysoevicha. Upon completion, the church was decorated with paintings, made by Moscow masters. During a fire in 1670 the monastery suffered again. In 1676 the cathedral church to the north was built winter church with a bell tower, which was consecrated in honor of the Metropolitan of Moscow Alexy. In 1736, at the request of abbot of the monastery of Jonah and the decree of Archbishop Jehoiakim attributed to Afanasyevsky monastery chapel attached to his or Znamenskaia Vlasievskaya Tower, which is the entrance gate to the earthen city. Today it is known as Znamenskaya Church.

Afanasievskiy Monastery significant've never been in the richness of their possessions, or by the number of monks: in 1717 there lived only seven monks but one Belec; the staff has not increased, and according to the 1802 territory of the monastery was quite small, it was limited to a low stone wall just to the east and northeast. On the other side of the fence as a monastic outbuildings were narrow-minded homes, as well as the Saviour Proboinskaya church.

ET, front facade of the monastery, which is out on the break-out, in the 18th century. two stone towers erected a small size, one of them played the role of the Holy Gate, located in another chapel in honor of an important event - the finding of the miraculous icon here. Tower spiers ended with figures of trumpeting angels.

June 25, 1768 in the center of Yaroslavl, once again there was a fire. The list contained the damage, in fact, the first description of the monastery buildings Athanasian. During the restoration work has been updated painting temple Athanasius and Cyril, the original stone iconostasis was replaced with a wooden one.

In 1820-1830 gg. in the monastery were carried out large-scale work on its improvement: there were erected two-storeyed stone abbot's quarters with a refectory; They were built two sister cells; for the Church of Athanasius and Cyril in 1825 tradesman Constantine missal produced at his own expense a new iconostasis, Alexander Charyshnikov from Yaroslavl gilded it; in 1831, the temple was decorated with warm paintings, murals executed Timothy Medvedev. At the same time, single-tiered bell tower was rebuilt on the porch warm church of the monastery abolished Borisoglebskii parish was transferred to a 115-pood bell. The ensemble of the monastery bell tower of seven bells.

The next surgery Afanasievskiy monastery was at the turn of 19-20 centuries .: in 1897 were built of stone cellars, coach, barn, bathhouse, stables; in 1903 and 1907. carried out repair work in the cathedral church of the funds allocated to FE Vakhrameev; in 1912 was ponovlena mural painter and restorer MI Dikareva on donations AI Vakhromeeva.

In 1764 by decree of Empress Catherine II the monastery Afanasievskiy ranked as unimportant. December 12, 1857 Afanasyevskaya monastery was built in the degree treteklassnoy, her superiors had since that time the rank of Archimandrite. Since 1895 Afanasievskiy monastery received the status of residence of the vicar bishop of the Diocese of Yaroslavl.

After the Revolution, when the monastery was founded Afanasyevsky parish community. In February 1925, the monastery was closed, 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 city authorities bell tower was demolished and the church Athanasius and Cyril, and other monastic buildings housed the organization, production workshops, fraternal body was used as a shelter.

In November 2007, a temple with a fence and gate towers, the Saints gave the Russian Orthodox Church. When the Yaroslavl Theological Seminary moved to the manor house Vakhromeeva by order of Bishop Cyril monastery church became a seminary. 31 January 2008 in the chapel Alexy was committed first service.