In the middle of the 17th century, the village of Kutukovo was part of the patrimony of the Goritsky Monastery in Pereslavl-Zalessky, and after the abolition of the monastic patrimony, it was transferred to the state department. In the patriarchal tax books of 1656, the Church of St. Nicholas the Wonderworker is noted in this village; the subsequent fate of this church is unknown.
The existing stone church in the village of Kutukovo was built with funds from parishioners in 1833. The stone bell tower was built at the same time as the church.
In 1968, the temple received the status of an architectural monument. After restoration in the 1980s, the former church housed the repository of the Central State Archive of Film, Photo, and Fond Documents of the RSFSR. After 1992, the archive was removed, and the church building was returned to believers.