Shin-Aomori Station is the northern terminus of the Ōu Main Line from Fukushima via Akita (a distance of 486.3 km (302.2 mi)), although most trains continue to Aomori.

It also forms the northern terminus of the high-speed Tōhoku Shinkansen line from Tokyo (a distance of 674.0 km (418.8 mi)), operated by JR East, and the starting point of the Hokkaido Shinkansen to Shin-Hakodate-Hokuto (a distance of 148.9 km (92.5 mi)), operated by JR Hokkaido.

The conventional Ōu Main Line has a single island platform, serving two tracks.

The Shinkansen portion of the station, which opened on 4 December 2010, consists of two elevated island platforms serving four tracks.

Work on a new station building began in July 2007, and was completed in 2010 ahead of the opening of the Tōhoku Shinkansen extension on 4 December 2010.