Real estate agents purchased the private property in the area by telling residents and local government officials that the land was needed to build a
Nissan/
Ford motor vehicle factory which would provide increased employment. Actually, however, the agents were in league with JNR and national politicians from the LDP party to acquire the land for the proposed station, which was not disclosed to the public at this time. The subterfuge was subsequently exposed in a novel and popular film called . The police opened several investigations, but the suspected agents, JNR employees, and political staffers fled the country until the statute of limitations on the alleged crimes expired. Shin-Yokohama Station opened on 1 October 1964, with the opening of the Tokaido Shinkansen. At the time, the surrounding area was completely rural, and the site was selected as it was the intersection of the Tōkaidō Shinkansen tracks with the existing Yokohama Line. The station was connected to the Yokohama Municipal Subway system on 14 March 1985. With the
privatization of
JNR on 1 April 1987, the JNR portion of the station came under the operational control of JR East. The station building was remodeled in 1998.
Station numbering was introduced to the Yokohama Line platforms 20 August 2016 with Shin-Yokohama being assigned station number JH16.
Sōtetsu–Tōkyū Link Line The Sōtetsu–Tōkyū jointly operated Shin-yokohama Station opened on 18 March 2023 is one of the major infrastructures of the Eastern Kanagawa Rail Link project to improve the regional access to the Shin-Yokohama Shinkansen station by rail, which was previously only accessible via the JR Yokohama Line and Municipal Subway Blue Line. As a response to the new railways, JR Tokai started a new limited Nozomi service departs from Shin-Yokohama for and on the same day as the opening of the Sōtetsu–Tōkyū Link Line. Because the Sōtetsu–Tōkyū platform level is directly 2-story underneath the Municipal Subway Blue Line platform, the subway platforms were
underpinned to fortify the foundation. The operation of the subway Blue Line was not obstructed during the construction of the new station. All the involved construction parties were commended by the
Japan Society of Civil Engineers in 2020 for commencing such a difficult task. File:Construction of Shin-Yokohama Station (Shin-Yokohama Line) 01.jpg|View above the construction site ==Passenger statistics==