Shin-koenji Station is served by the Tokyo Metro Marunouchi Line from Ogikubo to Ikebukuro, and is 21.5 km from the eastern terminus of the Line at Ikebukuro.

The station consists of two underground side platforms serving two tracks on the first basement level.

[2] The station facilities were inherited by Tokyo Metro after the privatization of the Teito Rapid Transit Authority (TRTA) in 2004.

[2] Its two exits are on either side of Ōme Kaidō Avenue, a major road connecting Shinjuku to the western suburbs of Tokyo.

The north exit is adjacent to Look Shōtengai, a pedestrian shopping street popular for its used clothing and music stores.