For almost three centuries, the site where the Filaretov School was later established housed the Zaborov Monastery's courtyard. This monastery, one of the oldest in Moscow, was located in the Kremlin but was destroyed by the Bolsheviks in the early 1930s. The Small Kharitonyevsky Lane was called Zaborovsky until the 19th century, and the lane leading to the courtyard was named Chudovsky. During the Soviet era, it was renamed, and in modern times it became known as Ogorodnaya Sloboda, in memory of the gardeners' settlement that existed here until the 18th century.

The monastery courtyard, founded in the 1670s, existed until the mid-19th century. After its dissolution, the Filaretov Eparchial School was established here. The wooden buildings were dismantled, and in 1861, a two-story house was built in their place according to the design of architect A.O. Vivien. It was a building with simple architecture and a modest facade. The school moved here in 1865. In 1878, architect M.G. Piotrovich added a third floor. Inside, a house church dedicated to Filaret the Merciful was arranged, which operated until 1919 when it was closed by the Bolsheviks.

The Filaretov Women's Eparchial School was founded in 1832 at the initiative of Metropolitan Filaret of Moscow and Kolomna for the education of young women of spiritual rank. Initially, it existed as a training division at the Gorikhvostov Charity House in the estate of the Gagarins-Tyutchevs on Armenian Lane. The school was managed by the Moscow Guardianship for the Poor of spiritual rank. Maria Pavlovna Chekhova, the younger sister of the writer, studied here, although her education was paid for by the Taganrog merchant Sabinnikov, as the Chekhov family had no means.

After the 1917 revolution, the Filaretov School was closed. The building housed the Internal Security Administration of the Cheka-OGPU, and in 1925, it came under the jurisdiction of the Soviet Navy. At the turn of the 1920s-1930s, the building was reconstructed according to the design of architect P.A. Golosov, and a grand portico appeared.

Currently, the property belongs to the Ministry of Defense, and it houses the Logistics Headquarters of the Armed Forces of the Russian Federation.