The parish was established in 1889;[3] staffed by the Salesians of Don Bosco from 1979 to 2003; and closed in 2003 because of a diminished congregation and structural problems.

In 2013, the premises at 260-262 W. 118th St., southwest corner of St. Nicholas Avenue, in Harlem, Manhattan was sold to a private developer.

[1] In 1897, Father Keogan purchased St. Michaels's Episcopal Church and used it for services until St. Thomas was completed; after which he turned it into the parish school for 900 students, staffed by the Sisters of Mercy.

The AIA Guide to NYC describes the church as follows: “No name is to be found on this church, but its finely detailed neo-Gothic façade, prominently entered via a stairway and an arcaded porch, demands attention.” The building is a blend of English Perpendicular Gothic, Moorish and Venetian Gothic, in what is described as “berserk eclecticism”, “unnameable but wonderful.”[5] The interior had intricately carved woodwork; the altar was of white marble.

We are growing.’ The posters call St. Thomas ‘the Catholic Church in Harlem with room for you!’”[6] In addition, there were dubious cracks in the main internal columns.

However, the stained glass was removed to the new Church of Blessed Kateri Tekakwitha in the upstate New York town of Lagrangeville.

[2][8][9] In 2013, a developer, Artimus, bought the former church and rectory, and proposed partial demolition, a theater, and a housing condominium.

Ann Friedman of the New York Landmarks Conservancy said that it was felt that "community re-use of at least some of the church was better than seeing it demolished.

[4] The adjacent 1907 rectory was renovated into an artist's home and studio, featured in The New York Times Style Magazine in 2023.