Tsugaruishi Station is served by the Rias Line, and was located 82.8 rail kilometers from the terminus of the line at Sakari Station.

The station was absorbed into the JR East network upon the privatization of the Japan National Railways (JNR) on 1 April 1987.

The station was destroyed during the 11 March 2011 Tōhoku earthquake and tsunami.

A KiHa 100 series train, which was at the station at the time, was also derailed and destroyed.

As of 2018, the station has been rebuilt along with the rest of the closed segment of the Yamada Line.