In the patriarchal accounting books, the Sign Church is not mentioned among the churches of Pereslavl. However, since all churches that paid church tax to the patriarchal treasury had to be recorded, it is likely that the Sign Church is listed under another name. In the books from 1628 to 1746, there is mention of the now non-existent Church of the Nativity of John the Baptist in Pereslavl. Some churches from the 17th century, now disappeared, have survived as chapels in other churches, for example, the chapel of Saint Apostle Philip at the Assumption Church. Considering that only the Sign Church has a chapel in honor of the Nativity of John the Baptist, it can be assumed that this name refers to the current Sign Church. It is known that the Church of the Nativity of John the Baptist existed even before the 17th century. The life of the Venerable Daniel of Pereslavl states that he asked Grand Duke Ivan Vasilyevich IV to restore the dilapidated church, indicating its existence in the early 16th century. In the 17th century, it paid a tax of four altyns with money in 1628, and in 1653, 1 ruble, 2 altyns, and 2 dengi.

During the time of Peter the Great, the Church of the Sign of the Most Holy Theotokos was known in Pereslavl, located 'by the ships.' This name is explained either by the presence of a shipyard or by the storage of ships on the shore after Peter the Great left Pereslavl. By the early 18th century, the Sign Church already existed in Pereslavl, which continued to be referred to as the Nativity of John the Baptist in patriarchal and synodal books until 1746. This wooden church was replaced in 1788 by a stone temple built by the widow of Major Anna Ivanovna Maslova. The appearance and interior decoration of the church have significantly changed since then. The church has two altars: in the cold part in honor of the Sign of the Most Holy Theotokos, and in the warm chapel in honor of the Nativity of John the Baptist. The church is richly supplied with utensils, vestments, holy icons, and liturgical books, some icons adorned with silver-gilded vestments and pearls.

Church documents are preserved intact, including copies of metric books from 1795 and confession lists from 1800. A special clergy has existed at the church since 1879, consisting of a priest and a psalmist. Their maintenance is provided by the interest from the clergy's capital, income from services, and rent from the church shop, totaling about 620 rubles per year. There are church houses for the clergy. The land by the church amounts to 458.5 fathoms, with an additional 483 square fathoms purchased in 1882. There is a capital of 1,000 rubles for the repair of church houses. The church owns a wooden shop, rented out for 102 rubles a year. The parish consists of 43 men and 45 women, all Orthodox. Since 1863, a church-parish school has been operating at the church, which had 25 students in 1893.

The church was closed in 1929 and demolished in 1935, and a wine shop was built in its place. In 1998, the shop was dismantled, and a new Sign Church was erected on the old site, consecrated in 2004. The modern temple is built in the Russian style and consists of a five-domed square, a refectory, and a tented bell tower. The second altar is dedicated to the Tsar-Martyr and the New Martyrs of Russia.