The monastery was founded during the emergence of new monasteries in the late 14th and early 15th centuries by followers of Sergius of Radonezh. In 1397, monk Kirill of Belozersk dug a cave on the shore of Lake Siverskoye, marking the beginning of the future monastery's history. His companion, Ferapont of Belozersk, later founded the nearby Ferapontov Monastery. The rule of the Belozersk monasteries was characterized by particular strictness.

In the context of Moscow's rivalry with independent Novgorod, the Kirillo Monastery became an important stronghold for consolidation in the Zavoloche region and a major economic center. It was on the trade route to the north to the White Sea, where various trade flows intersected. Until the times of Peter the Great, the monastery actively traded, especially in salt and fish.

Many of the preserved churches were built of stone at the end of Vasily III's reign. In 1528, he visited the Kirillo Monastery with Princess Elena Glinskaya to pray for an heir. The birth of a son, the future Tsar Ivan the Terrible, was associated with the intercession of St. Kirill of Belozersk. Ivan Vasilyevich maintained a special attachment to the monastery throughout his life, considering it his savior. Before his death, having accepted the schema, the first Russian tsar, like his father, became a monk of the Kirillo-Belozersky Monastery.

The monastery grew richer and expanded, despite a fire in 1557, becoming the largest center of stone construction in the north of the Russian state and the second-largest ecclesiastical landowner after the Trinity Monastery. It owned 607 villages. The abbots of Kirillov held important positions in the church hierarchy and often moved to significant archbishoprics.

In 1722, Peter I visited the monastery. By that time, the monastery owned 21,000 peasants in 16 districts, but with the opening of Baltic ports and the decline of northern trade through Arkhangelsk, its economic significance decreased.

The gradual decline of the monastery continued under subsequent rulers. In 1764, by decree of Catherine II, the monastery lost its peasants and lands. Twelve years later, the monastery settlement was transformed into the town of Kirillov, and the city and district prison was placed within the fortress wall.

In 1997, for the 600th anniversary of the monastery, part of its territory was transferred to the Vologda Diocesan Administration. In 1998, the Orthodox religious organization Kirillo-Belozersky Men's Diocesan Monastery was registered.

By the decision of the Holy Synod on October 10, 2009, Hieromonk Ignatius Molchanov was appointed the abbot of the monastery. However, on October 22, 2015, he was relieved of this position and appointed as the abbot of the Spaso-Prilutsky Monastery in Vologda. Since December 14, 2015, Hieromonk Anastasius Dodarchuk has been acting as the abbot.

To this day, the iconostasis of the Assumption Cathedral has been almost completely preserved, which is unique in the history of Russian art. The ancient icons had long been scattered: of the 60 surviving, 33 were in Kirillov, while the others were in the Russian Museum, the Tretyakov Gallery, and the Museum of Andrei Rublev. In April 2009, some icons were returned to Kirillov.

In the church of Kirill, the relics of St. Kirill of Belozersk lie beneath the ground, the main shrine of the monastery.

In April 2019, it became known that the Ministry of Culture of Russia would transfer to the monastery for five years an ark containing relics of 20 saints. The monastery plans to create a new silver cover for the ark, after which the relics will be transferred to the church of Kirill of Belozersk.