[5] The station sits beneath Grand Central Terminal, which serves the Metropolitan Transportation Authority (MTA)'s Metro-North Railroad.

The new terminal enables passengers to transfer to Metro-North's Harlem, Hudson, and New Haven Lines, as well as the New York City Subway at Grand Central–42nd Street station.

[12] Grand Central Madison also provides an alternative route from the east side of Manhattan and from Metro-North lines to John F. Kennedy International Airport, via a connection with the AirTrain JFK people mover at the Jamaica station.

[13] Formal proposals to bring Long Island Rail Road trains to the east side of Manhattan date to 1963.

[15] After people living near the proposed transportation center objected, the MTA's board of directors voted to route LIRR trains to Grand Central by 1977.

[17] The East Side Access project was restarted after a study in the 1990s showed that more than half of LIRR riders work closer to Grand Central than to Penn Station.

[25] The LIRR received operational control of Grand Central Madison on December 9, 2022, upon which the station and tracks became subject to Federal Railroad Administration regulations.

[32][33][5] The initial service was a shuttle, known as Grand Central Direct, to and from Jamaica station, with some trains running express and others making intermediate stops at Woodside, Forest Hills, and Kew Gardens.

[39] In March 2024, Tracks Raw Bar and Grill became the first commercial tenant to sign a lease at Grand Central Madison.

[49] In December, UNESCO gave its 2024 Prix Versailles Interior Award to Grand Central Madison, calling the station one of the world's most beautiful.

[50] At the end of 2024, the storefronts at Grand Central Madison remained vacant, and Tracks Raw Bar and Grill had not yet opened.

An MTA spokesperson said the rule was an extension of an existing restriction at Grand Central Terminal and that "a customer should not have to wait more than 90 minutes to catch their train, barring a significant service disruption".

[71] The other four, one level down in the LIRR mezzanine, are: The Presence, a landscape with a deer; The Sound, a seascape with a gull; The Spring, featuring four turkeys; and The Water's Way, a beach scene.

[71] The Madison Concourse level also holds an even larger 120 ft-long (37 m) mosaic by Yayoi Kusama: "A Message of Love, Directly from My Heart unto the Universe".