Kikuna Station was opened on February 14, 1926 as a station on the privately held Tokyo-Yokohama Railway Company (the predecessor to the Tōkyū Tōyoko Line). The Japanese Government Railways (the predecessor to the JNR) began operations to Kikuna on September 1 of the same year. All freight operations were suspended from 1970. In 1972, Tōkyū Tōyoko Line portion of the station was rebuilt, with new elevated tracks and a new station building; however, the tracks remained unused until the Tokyo Metro Hibiya Line connected to the station in 1988 (which was then discontinued on 15 March 2013 when the Daikan-yama to Shibuya section of Tōkyū Tōyoko Line was moved to underground and with through running to Tokyo Metro Fukutoshin Line began). With the privatization of the JNR on April 1, 1987, the JNR portion of the station came under the operational control of JR East. The Tōkyū Tōyoko Line platforms were lengthened in 1991 to accommodate seven-car trains; with through running with Fukutoshin Line, the platforms were lengthened again to accommodate ten-car trains.
JR Kikuna Station has a single island platform serving two elevated tracks, connected to the station building and the Tōkyū Tōyoko Line by an underpass. Tōkyū Tōyoko Kikuna Station has two island platforms serving four tracks.