It was founded around 1330 by a Tatar convert, Prince Chet, whose male-line descendants included Solomonia Saburova and Tsar Boris Godunov, and is dedicated to St. Hypatios of Gangra.

The legend says that he was miraculously cured from a disease by a vision of the Virgin Mary and St. Philip and St. Hypatius, and decided to build the monastery as a sign of gratitude.

During the Time of Troubles in Russia, the Ipatiev Monastery was occupied by the supporters of False Dmitriy II in the spring of 1609.

A private house of Mikhail Romanov was restored on the orders of Tsar Alexander II, though the authenticity of the reconstruction was questioned by Konstantin Pobedonostsev .

In September 2002, one of the most prominent museum exhibits, the large wooden church (1628) from Spas-Vezhi village, was destroyed by fire.