The stone church in honor of the great martyr Nikita in the Nikita Monastery has existed since ancient times, but by 1528 it had fallen into disrepair and was dismantled by the order of Grand Duke Vasily Ivanovich. Vasily III allocated funds for the construction of a new church, but it was small and soon became part of the new cathedral. In 1561, Ivan the Terrible decided to dismantle the old church built by his father and erect a new one over the grave of St. Nikita the Blessed. The new stone cathedral was built around the church of Nikita the Stylite, the first stone church of the monastery, and the old church became the southern chapel of the cathedral. Later, a northern All Saints chapel was added to it. Thanks to the support of the tsar, construction progressed quickly, and in 1564 the cathedral was completed. The consecration was attended by the tsar, Tsarina Maria, Tsarevich Ivan, and Metropolitan Athanasius. Initially, the cathedral's roof was wooden, but in 1686 it was covered with white iron, and in 1764 it was replaced with an iron four-pitched roof, removing the arches of the zakomar. In 1759, the windows were enlarged. Until the mid-18th century, the cathedral remained unpainted, and only in 1764 was it adorned with paintings. In 1838, the painting was updated, but unsuccessfully, and in 1876 it was redone by academic painter Gribov.

After the monastery was closed in 1923, valuable items from the cathedral were transferred to the Pereslavl Museum, and the cathedral itself was used for purposes other than its intended use. Various institutions were located on the monastery grounds, which did not care for the preservation of the monuments. As a result, the cathedral and other buildings suffered greatly. In 1933, the unique iconostasis of the cathedral was destroyed. Restoration work that began in the 1960s and 70s did not benefit the cathedral, and in 1984, due to the restorers' mistakes, the central dome collapsed. For several years, the church stood without a dome, exposed to the elements. The dome has now been restored, and the foundation strengthened. By 2013, the cathedral had been externally restored, but work on the painting of the walls and vaults continues under the guidance of the Palekh artist Sergey Grigoryevich Morozov.