The village of Ilysk began its history in 1863 with the founding of the Ilysk stanitsa, which was part of the Abinsky regiment. The first archpriest was Yefim Petrovich Timofeyevsky. In the same year, a chapel was built in the square of the stanitsa, and a year later, a prayer house in the name of St. Nicholas appeared in its place, which was a wooden building. The church clergy were allocated 150 desyatins of land, of which 50 desyatins were church property.

Ten years later, in 1873, the Church of St. Nicholas was built. The military allocated 10,000 rubles for its construction, while the parishioners collected 6,000. The church, although wooden, stood on a stone foundation, had the shape of a basilica, two domes, and a tent-shaped bell tower. The altar was painted by icon painters from Palekh and the Trinity Lavra. In 1896, the church was expanded with public and church funds. The clergy, increased in 1893, included two priests, a deacon, and two psalmists. The names of the priests known from preserved documents are: Georgy Semyonovsky (1867), Stefan Klyuchevsky (1869), Fyodor Karpinsky (1887), Lev Dmitrievich Chalenko (1890), Dmitry Ivanovich Mikhailov (1910).

With the advent of Soviet power, life in the stanitsa changed. In 1933, the destruction of churches in the Seversky district began. The first to be destroyed was the church of the Grigoryevskaya stanitsa, and the last ones in 1939 were the churches of Ilysk and Seversk. The St. Nicholas Church was turned into a reading room, then into a cultural house. Priests were also persecuted. According to a report from the regional court dated May 25, 2006, Mikhail Timofeevich Estratov, a native of the Novotroitskaya stanitsa, who served as a priest in the Nikolayevskaya church, was arrested on January 30, 1938, and sentenced for participating in a counter-revolutionary church-monarchist organization. He was shot on February 8, 1938, but was fully rehabilitated in 1956.

After the war, the church building was used as a House of Culture. On August 12, 1990, at a meeting of the residents of Ilysk, it was decided to transfer the building to the believers for a church until October 1, 1990, to move the dance floor, to transfer part of the adjacent land and the watchman's building to the church. This proposal was unanimously supported.

In August 1990, the Seversky RIK registered the community of the Russian Orthodox Church in Ilysk, and in May 1991, a land plot of 6,100 sq. m. was allocated. The main altar of the church was consecrated in honor of St. Nicholas the Wonderworker, and the right altar, in honor of the icon of the Kazan Mother of God.