The warm Annunciation church with a refectory was built on the initiative of Tsar Ivan the Terrible, like the Nikitsky Cathedral, but probably a little later. In the land books of 1629-30, it is mentioned as "Another warm church with a stone refectory of the Annunciation of the Most Holy Theotokos, and the chapel of Theodore Stratilates." Under the refectory were the bakery and kitchen, and beneath them, the cellars.

Over the centuries, the Annunciation church has undergone significant changes. The chapel in the name of St. John Climacus was abolished, and in its place a sacristy was arranged. The chapel of the Great Martyr Theodore Stratilates was also altered, re-consecrated in the name of St. Nicholas the Wonderworker, and is now separated from the main church by two arches. The refectory was reduced by half, with part fenced off for the abbot's quarters. It is believed that Peter I stayed in these quarters during his first visit to Pereslavl on Lake Pleshcheyevo. Adjacent to the refectory is an octagonal bell tower built in 1668 during the reign of Tsar Ivan the Terrible, but it was severely damaged during the Polish siege of the monastery in 1611. It was restored in 1668 with funds from Tsar Alexei Mikhailovich and his wife Maria Ilinichna. The iconostasis of the church has also been remodeled several times. The first iconostasis lasted until 1766, when it was replaced with a new one in a modern style. In 1809, the iconostasis was updated again.

In 1878, historian A. I. Svirilin described the Nikitsky Monastery and noted that the iconostasis of the Annunciation church did not represent archaeological interest. He mentioned that only the temple icon of the Annunciation of the Most Holy Theotokos remained, donated in 1696 by Archimandrite Arsenius of the Chudov Monastery. In the 1870s, with the help of benefactors, a mosaic floor was laid in the church, and a new oak iconostasis was installed in the Nikolsky chapel. During this time, the walls of the church were decorated with paintings. The wooden roof of the church lasted longer than that of the Nikitsky Cathedral and was only replaced with an iron one in 1851. During the Soviet era, the church suffered greatly, as it was constantly occupied by various institutions. In 1977, a fire occurred in the building that housed a driving school, destroying all wooden structures. The metal connections broke, and cracks appeared in the walls and vault. Restorers working in the monastery in the 1960s-70s aimed to turn it into a tourist center of the "Golden Ring" of Russia. However, after the collapse of the central dome of the Nikitsky Cathedral in 1984, interest in the monastery waned, and it, like the Annunciation church, was left to its fate.

In December 1993, the monastery reopened. The restorers and residents were faced with a sad sight, but with God's help, restoration began. The work was overseen by the monastery's abbot, Bishop Anatoly Aksyonov, until 1999. The Annunciation church was restored in 1999 under the supervision of Archimandrite Dmitry Kramtsov of the Nikitsky Monastery. In 2000, with the blessing of Patriarch Alexy II, the relics of Nikita the Stylite, who was killed in 1186, were extracted from the ground and solemnly transferred to the restored church, where they are kept along with his chains. The church is now fully restored and services are once again held there.