It was constructed from 1899–1909 and was built by the Latin Rite Catholic community in a Gothic type construction, by Kyiv architects Vladislav Horodetskyi and Emilio Sala. It stands at vulytsia Velyka Vasylkivska (Greater Vasylkiv street) in Pechersk District closer to the National Sports Complex Olimpiysky and the Railroad station.
A competition was held in 1898 for the designs for a Roman Catholic church in Kyiv, which was won by architect Stanislav Volovskiy. His entry into the competition included a Gothic type construction with two 60 m (197 ft) towers. The final revision and management of the project was assigned to the Kyivan architect Vladyslav Horodetskyi, and Emilio Sala added sculptural decoration in artificial stone to the construction. To increase the stability of the construction on the uneven Kyiv ground, it was ensured by bore-and-stuffed piles, a newly introduced invention of Anton Strauss. The construction work was carried out by exclusively from voluntary donations, and lasted for ten years (1899–1909).
In 1909, the church was consecrated in the name of Saint Nicholas, however the construction was not yet completed. A Gothic style three-story house was built for the parish clergy to the left of the church. In 1938, Soviet authorities closed the church after its Roman Catholic priest was "absent" for two years due to the Soviet persecution of Christians.

For some time after its closure, the building was used by the punitive organs for technical purposes, and, at some point, served as a KGB service building. After its restoration in 1979-1980 the church was turned into the National House of Organ and Chamber Music of Ukraine. For the reconstruction and restoration of the severely damaged church, the building's stained glass windows were manufactured in the Baltics, its furniture was created in Lviv, and the high-quality wood floors were produced in the Ivano-Frankivsk province. The company, Rieger-Kloss then located in Czechoslovakia, manufactured an organ for the church. Its manufacturer tried to architecturally tie the organ to the building itself.