Tsubata Station is served by the IR Ishikawa Railway Line between Daishōji and Kurikara, and lies 11.5 km east of Kanazawa.

The station consists of two island platforms serving four tracks, connected by a footbridge.

[1] With the privatization of Japanese National Railways (JNR) on 1 April 1987, the station came under the control of JR West.

[1] From 14 March 2015, with the opening of the Hokuriku Shinkansen extension from Nagano to Kanazawa, local passenger operations over sections of the Hokuriku Main Line running roughly parallel to the new shinkansen line were reassigned to different third-sector railway operating companies.

[2] From this date, Tsubata Station was transferred to the ownership of the third-sector operating company IR Ishikawa Railway.