Jimmuji Station has two side platforms serving two tracks. The platforms are connected by a level crossing for passenger use. A dedicated entrance and exit is provided on the north side of the station for US Navy personnel, which links directly to the adjoining Ikego housing complex.
On the north side of the station are narrow gauge (1,067 mm (3 ft 6 in)) storage tracks used for transferring rolling stock from J-TREC's Yokohama factory to JR East's tracks at Zushi Station.
Jimmuji Station opened on April 1, 1931, as a temporary stop on the Shōnan Electric Railway, the predecessor to the current Keikyu. It was initially located 300 meters towards Kanagawa Hakkei than the present station. It became a full station on June 11, 1936. In 1942, the Shōnan Electric Railway became part of the Tokyu Corporation, and Jimmuji Station was relocated to its present address on September 1, 1944. In 1948, the Keihin Electric Railway (later Keikyu) spun out from the Tokyu Corporation. A new station building was completed in March 2007.