Yamato Station was opened on May 12, 1926 as a station on the Jintsu Railway. The Odakyu Station was opened on April 1, 1929 slightly to the west of the existing station, and was named Nishi-Yamato Station (西大和駅,Nishi-Yamato-eki?). On June 1, 1944, Yamato Station was relocated to become adjacent to Nishi-Yamato Station, with the new joint station taking the name “Yamato Station”. The station building was completely reconstructed in a multiyear project beginning from 1986. In 1993, the tracks and platform of the Sagami Railway were relocated to a subway level, which created room for expansion of the Odakyu station to two platforms in 1996.
Yamato Station is a joint use station. The north exit is operated by the Sagami Railway and the south exit is operated by the Odakyu Railway, although passengers can use either exit regardless of what line they are using. The Odakyu Railway station consists of two island platforms connected by an overpass to the station building. The station building is elevated, and located above the platforms and tracks. The Sagami Railway station has one island platform, located underground.