Ōbarino Station consists of a single side platform serving bi-directional traffic, connected to the station building by an overpass. The tracks of the Akita Shinkansen run in between the station building and the platform.
Ōbarino Station opened on February 1, 1950. It has been unattended since December 1, 1979. The station was absorbed into the JR East network upon the privatization of JNR on April 1, 1987. A new station building was completed in April 2006.