Izuhakone Railway
JR Mishima Station has two island platforms serving tracks 1 to 4. Track 2 and Track 3 are the primary tracks for the Tōkaidō Main Line, with Tracks 1 and 4 used for through passage of express trains. The Tōkaidō Shinkansen uses Tracks 5 and 6, which are served by a separate island platform. The adjacent Izuhakone Railway has one side platform and two bay platforms serving Tracks 7, 8 and 9. All platforms are connected by an underpass to a central concourse leading to the station building. The station building has automated ticket machines, TOICA automated turnstiles and a staffed ticket office.