Higashi-Shinjuku Station is served by the Toei Oedo Line and the Tokyo Metro Fukutoshin Line.

The Tokyo Metro station has two island platforms each serving two tracks, with platform 1/2 (southbound) on the fifth basement ("B5F") level and platform 3/4 (northbound) on the sixth basement ("B6F") level.

Non-stop trains (Express and Commuter Express) pass stopping (Local) trains at this station.

[1] The Tokyo Metro Fukutoshin Line part of the station opened on 14 June 2008.

[1] The two Tokyo Metro island platforms initially used only one track each, with the second tracks for passing non-stop trains hidden behind screens.