Hon-komagome Station is served by the Tokyo Metro Namboku Line, and lies 13.6 km from the starting point of the line at Meguro.

Many train services continue to and from Hiyoshi in Kanagawa Prefecture on the Tokyu Meguro Line in the south and to and from Urawa-Misono in Saitama Prefecture on the Saitama Rapid Railway Line in the north.

The station is an underground station, with the ticket machines and ticket barriers located on the first basement ("B1F") level, and the platforms on the third basement ("B3F") level.

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

[2] In fiscal 2019, the station was used by an average of 22,933 passengers daily.