The history of the church of the holy martyr Antipius in Kolymazhny Yard dates back to the 16th century. The stone church was built in the Konyushennaya Sloboda around 1530. The name of the church is related to its location: "at the large stables", "in Chertolye", "near the Tsar's large stables".

The Church of Antipius is notable for having two altars: one in the name of the holy martyr Antipius and a small altar in the name of Saint Gregory of Decapolis. According to legend, the small altar was built by Gregory Lukyanovich Belsky, known as Malyuta Skuratov, whose courtyard was nearby.

Saint Antipius is known as a healer who helps with toothache. This is the only church in Moscow dedicated to Antipius, which attracted many Muscovites suffering from tooth pain. People from different classes and parts of the city came here to pray. Among the parishioners were the Lopukhins, the Apraxins, the Obolenskys, and in the early 20th century, the artist Valentin Serov, who lived nearby.

In the 18th century, chapels were added to the church: Saint Nicholas the Wonderworker (in 1722), Great Martyr Catherine (in 1773), and the Nativity of John the Baptist (in 1798).

In 1912, the Museum of Fine Arts named after Emperor Alexander III opened opposite the church, and since then, the fates of the museum and the church have been closely intertwined.

After the revolution, in 1929, the church was closed, and the building was transferred to the Central Art Courses of the Association of Artists of the Revolution. It was used for a long time as a dormitory, and later housed restoration workshops and the storage department of the Pushkin State Museum of Fine Arts.

During the Soviet period, the building was not repaired and was in poor condition. In the 1950s, the dome and the head of the southern chapel of Saint Nicholas were destroyed.

In the 1960s, restoration of the church began under the guidance of architect L.A. David. It was planned to demolish all parts that appeared in the 17th-19th centuries, but this was opposed by the A.S. Pushkin Museum, which rented the building.

In the 1990s, another restoration was started. In 1991, a church community was formed, but it was only in 2005 that the church was successfully transferred to the Russian Orthodox Church.