Shin-Ōkubo Station is served by the circular Yamanote Line, with trains running every four minutes during the daytime off-peak.

The elevated station consists of a single island platform serving two tracks.

However, the freight yard plan was later abandoned, and the Seibu extension opened in 1952 with no stop at Shin-Ōkubo.

On 26 January 2001, a 47-year-old photographer from Yokohama and a 26-year-old Korean student died at the station when they were hit by a Yamanote Line train while trying to save a drunken Japanese man who had fallen off the platform onto the tracks and was also killed in the accident.

[11] The Korean student's life story formed the basis for the film 26 Years Diary, released in 2007 in Japan and in 2008 in Korea.