The Intercession Monastery, founded in 1410 by Prince Semyon Vladimirovich, who died from the plague in 1426-28, stood on the site of the church. In 1414, the venerable Pafnutiy took monastic vows there. He spent twenty years in the monastery and became its abbot in 1434. However, on April 23, 1444, Pafnutiy unexpectedly left the monastery and founded a new monastery on the Isterma River in honor of the Nativity of the Most Holy Theotokos. According to legend, his parents, Ivan and Fotiniya, were buried in the Intercession Monastery.

In the early 17th century, the monastery had two churches: a stone one in honor of the Intercession of the Most Holy Theotokos and a wooden one in honor of the Entry of the Lord into Jerusalem, as well as wooden cells. In 1610, Lithuanians and Poles ravaged and burned them. In 1615 and 1618, Tsar Mikhail Fyodorovich issued decrees ordering the restoration of the Vysokoye Monastery. A new wooden church of the Intercession of the Most Holy Theotokos and cells were built, adorned with church utensils from the Pafnutiy Monastery.

In 1764, as a result of the secularization of church lands, the Vysoko-Intercession Monastery became a parish church and was attached to the city’s Exaltation of the Cross Church until 1917. The area around it turned into a city cemetery.

At the turn of the 19th and 20th centuries, a chapel was erected near the altar, where, according to local tradition, the parents of Venerable Pafnutiy rest.

In 1932, the church was closed, and in 1950 it was transferred to the Balabanovskoye grain procurement point. In 1962, it was included in the list of architectural monuments and was not used.

Currently, the church has been handed over to the Russian Orthodox Church. It is the only monument of wooden architecture from the 17th-18th centuries in the Kaluga region.