The JR portion of the station has a single side platform, serving one track.

Atsugi Station was opened on 12 May 1926, as the terminus of Jinchū Railroad (神中鉄道), now Sagami Railway).

The Sotetsu Railway (currently the JR Sagami Line) linked to the station on 15 July 1926.

On 1 April 1927, the Odakyu Electric Railway built the adjacent Kawaharaguchi Station (河原口駅).

With the completion of Ebina Station on the Jinchū Railroad on 25 November 1941, operations to Atsugi were discontinued.