[1] The main East Japan Railway Company (JR East) station and the directly adjacent private railways have a total of 35 platforms, an underground arcade, above-ground arcade and numerous hallways with another 17 platforms (53 total) that can be accessed through hallways to five directly connected stations without surfacing outside.

Japanese government urban planner Kensaburo Kondo designed a major revamp of the station in 1933, which included a large public square on the west side completed in 1941.

These plans were suspended upon the onset of World War II but influenced the current layout of the station area.

Seibu abandoned its plan to use the building due to a lack of space for trains longer than six cars; the building is now known as Lumine Est and retains some design features originally intended to accommodate the Seibu terminal (in particular, a very high ceiling on the first floor and a very low ceiling on the second floor).

On 21 October 1968, 290,000 marchers participated in International Anti-War Day, taking over Shinjuku station and forcing trains to stop.

In May and June 1969, members of the antiwar group Beheiren carrying guitars and calling themselves "folk guerrillas" led weekly singalongs in the underground plaza outside the west exit of the station, attracting crowds of thousands.

On 5 May 1995, the Aum Shinrikyo doomsday cult attempted a chemical terrorist attack by setting off a cyanide gas device in a toilet in the underground concourse, barely a month after the gas attack on the Tokyo subway which killed 13, left 6,252 people with non-fatal injuries, severely injured 50 people, and caused 984 cases of temporary vision problems.

The station facilities on the Marunouchi Line were inherited by Tokyo Metro after the privatization of the Teito Rapid Transit Authority (TRTA) in 2004.

[9][10] In 2020, the east–west free passageway was opened, shortening the time required for pedestrians to pass between the east and west exits by 10 minutes.

[12] When the Keio Line extended to Shinjuku in 1915, its terminal was located several blocks east of the government railway (presently JR) station.

In July 1945, the terminal of the Keiō Line was relocated to the present location, though on the ground level, on the west side of Shinjuku Station.

This was because the trains faced difficulty in climbing up the slopes of the bridge over the governmental railway after one of the nearby transformer substations was destroyed by an air raid.

The terminus for the private Odakyu Odawara Line is parallel to the JR platforms on the west side and handles an average of 490,000 passengers daily.

This is a major commuter route stretching southwest through the suburbs and out towards the coastal city of Odawara and the mountains of Hakone.

The Metro Promenade in turn connects to Shinjuku Subnade, another underground shopping mall, which leads onto Seibu Railway's Seibu-Shinjuku station.

The figures below are the official number of passengers entering and exiting (except for JR East) each day released by each train operator.

[46][47] Contemporary British painter Carl Randall (who spent ten years living in Tokyo as an artist) depicted the station area in his large oil painting Shinjuku, exhibited at the National Portrait Gallery in London in 2013.