The area of present-day Ninohe was part of ancient Mutsu Province, and has been settled since at least the Jōmon period.

Inhabited by the Emishi tribes, the Nihon Shoki describes the penetration of the area by forces of the imperial dynasty in the late Nara period; however, it was not under effective control of the central government until the mid-Heian period.

In the early Meiji period, the town of Fukuoka and the villages of Jōbōji, Kindaichi, Gohenchi, Tomai, Ishikiridokoro, and Nisattai were established within Ninohe District on April 1, 1889 with the establishment of the modern municipalities system.

The modern city was founded on April 1, 1972, with the merger of the town of Fukuoka with the village of Kindaichi.

Ninohe has a mayor-council form of government with a directly elected mayor and a unicameral city legislature of 18 members.

In terms of national politics, the city is part of Iwate 2nd district of the lower house of the Diet of Japan.