Since 2010, the station has been jointly operated by the East Japan Railway Company (JR East) and the Aoimori Railway Company, a third sector, regional rail operator.

It was nationalized on 1 July 1906 and became a station of the Japanese Government Railways Tōhoku Main Line.

After the end of World War II, the JGR became the Japanese National Railways (JNR).

[citation needed] On 15 March 1954 an F-84 Thunderjet from nearby Misawa Air Base crashed on top of Noheji Station, destroying the station building and killing twelve people.

Passenger trains serve Noheji Station just under 17 hours a day from 6:24 am to 11:06 pm.