Though city residents and business owners embraced public transit, by the late 1800s public opinion of the elevated structure of the train system was on the decline. The sound of the passing trains was deafening, and the tracks loomed oppressively over pedestrians, regularly dropping debris on the sidewalks below.

The Interborough Rapid Transit Company (IRT), a private railway company, was incorporated in April 1902 and shortly after began construction on the first underground subway system in New York City. The Sixth Avenue El was closed in 1938, and the structure razed in 1939. The replacement underground line, known as the Independent Subway (IND) Sixth Avenue line opened between 1936 and 1940.

Named after its builders and original tenant, the Pennsylvania Railroad (PRR), Pennsylvania Station was designed and built in 1910 by architects McKim, Mead & White in the neoclassical Beaux-Arts style. Before then, the Pennsylvania Railroad ended just east of the Hudson River. As part of an effort to compete with the New York Central Railroad, which ended in Manhattan at Grand Central Terminal, PRR President Alexander Cassett announced in December 1901, plans to construct a tunnel under the river and a station on the west side of Manhattan just south of 34th Street.