The monastery got its name from the area where it was founded, previously known as "mountain," and from the cathedral church of the Assumption of the Mother of God. The foundation of the monastery dates back to 1590, when the elder Domnikiya, during the reign of Tsar Fyodor Ioannovich and Archbishop Ion of Vologda and Great Perm, became its first abbess. This is confirmed by two surviving documents, one of which is a petition from 1613 submitted by the abbesses to Archbishop Silvester.

The first stone building of the monastery, a one-story hospital wing, was constructed in the second half of the 17th century. In 1692 and 1699, the cathedral church of the Assumption of the Mother of God with a bell tower and the winter church of St. Sergius of Radonezh were built. In 1709 and 1714, the gate church of St. Alexius, the man of God, was constructed. By the end of the 1790s, the monastery was surrounded by a stone fence with four towers at the corners.

In 1792, a fire destroyed all the wooden buildings of the monastery, leading to the loss of many documents, and therefore little information about its history before the 19th century has survived. In 1824, Emperor Alexander I visited the monastery, and in 1826 and 1828, with his funds, a two-story abbot's house was built.

In 1860, by the decree of the Holy Synod, the Nikolaevskaya Ozeretskaya church was annexed to the Gorny Ascension Monastery. In the 1870s and 1890s, buildings for an orphanage and a diocesan women's school were constructed. Until the end of the 19th century, the monastery served as a place of exile for women for adultery and prostitution. In 1880, the bell tower was rebuilt, and in 1888, Bishop Theodosius transformed the orphanage into a diocesan women's school, which moved to a new building outside the monastery in 1903.

In 1918, the monastery was closed, but some nuns remained there until 1923-1924, when it was finally handed over for the needs of the Red Army. The Assumption Cathedral remained active until 1924. After eviction, some nuns settled in houses near the monastery. During the Soviet period, the territory of the monastery housed a transit prison of the NKVD and a military unit, and the monastery fence was destroyed.

In 1995, the restoration of the Assumption Church began, and since 1996, services have resumed there. The abbot's house and the orphanage building were used as shops and warehouses. On November 15, 2014, Metropolitan Ignatius of Vologda and Kirillov inspected the abbot's house and decided to establish the Gorny-Ascension Women's Monastery as an Archdiocesan residence. Within a year, the former abbot's house was prepared for the sisters' residence and the placement of the choir department of the Vologda Theological Seminary. On December 24, 2015, the Holy Synod of the Russian Orthodox Church decided to open the monastery and appointed nun Filareta Dorokhina as abbess. On December 26, Metropolitan Ignatius elevated her to the rank of abbess.

After the revival of the monastery, major repairs were carried out in several premises, part of the roof of the ancient building was replaced, a monastery farm was created, and icon painting and sewing crafts are being developed.