The Church of St. Nicholas in Starovagankovsky Lane has been known since the 16th century, when it housed the residence of the Nikolo-Peshnoshsky Monastery. The church has been rebuilt multiple times. By the end of the 17th century, it had three altars and two chapels: in honor of St. Sergius of Radonezh and the Forty Martyrs of Sebaste.

The modern stone church was built around 1759, when the site belonged to A.A. Menshikov. In 1782, the site was purchased by P.E. Pashkov, and then a bell tower was added to the church, followed by a stone fence in 1792.

The history of the church is closely linked to the history of the Pashkov House.

During Napoleon's invasion in 1812, the church suffered from a fire and was looted. However, by 1814, thanks to the efforts of the parishioners, it was restored and consecrated.

When the Pashkov House was occupied by the Noble Institute in 1843, the church became the house church of the institute, then of the 4th gymnasium, and finally "museum" after the Rumyantsev Museum was established in the Pashkov House in 1862.

Contemporaries recall that Gogol loved to pray in the church of the Noble Institute.

In 1896, the priest Leonid Mikhailovich Chichagov became the rector of the church, thanks to whom the church gained fame in Moscow. Today, it houses icons and wall paintings created by Father Leonid Chichagov.

Through the efforts of Father Leonid, St. Seraphim of Sarov was canonized. In 1898, Father Leonid took monastic vows at the Holy Trinity St. Sergius Lavra, and in 1937 he was executed at the Butovo firing range. In 1997, he was canonized as the holy martyr Metropolitan Seraphim (Leonid Chichagov).

In 1902, the church was renovated, and a bell tower of Pskov type was constructed according to the design of architect G.P. Yevlanov.

Since 1905, thanks to the efforts of the director of the Rumyantsev Museum I. Tsvetaeva, a Board of Trustees for St. Nicholas Church was established.

After the revolution, the church was closed, looted in 1926, and partially destroyed.

In the 1930s, the church was used as a warehouse for the Lenin Library.

Restoration and reconstruction of the church began in the 1980s under the guidance of architects A. Klimenko and B. Moginov.

In 1992, services resumed here, and the church was handed over to the Russian Orthodox Church.