The church was built in 1872 to Gothic Revival designs in brownstone by architect W. Wheeler Smith and "distinguished by an elegantly tapered spire that, according to John A. Bradley in The New York Times, 'many declare…the most beautiful in this country.'"

St Nicholas's was the New York City church attended by Theodore Roosevelt, and a memorial service was held for him on January 30, 1919.

Dr. Malcolm James MacLeod, later reneged on the church's intention to sell to the Rockefeller complex for as much as $7 million.

The governing body pitched the sale again in 1946,[4] and after "considerable public debate", a deal was made in 1949.

After the demolition of St Nicholas's, the bell was relocated to the New Middle Collegiate Church on Second Avenue, Manhattan.