The station is unique in design. It is a bi-level station, with an island platform on each level, but is not configured in the standard express-local lower-upper configuration (which is used in most stations south of this point). Instead, the upper platform serves northbound (uptown) trains and the lower level serves southbound (downtown) trains. North of the station, just after crossing the Harlem River, the line splits into the IRT Jerome Avenue Line (heading north) and the IRT Pelham Line (heading east). On the lower platform, each track comes from one line, and a flying junction south of the station allows trains to choose the local or express track. On the upper platform, the west track comes from the local track, and the east track comes from the express track; a flying junction north of the station splits the lines.
There is an active tower at the north end of the upper platform; it is a satellite to the tower at 42nd Street–Grand Central, which controls the entire length of the Lexington Avenue Line. This station's renovation was completed in 2005.