The area of present-day Futaba was part of Mutsu Province. The remains of Kofun period burial mounds have been found in the area. During the Nara period, it was the center of ancient Futaba District within Iwaki Province During the Edo period, it was originally part of Sōma Domain, ruled by the Sōma clan until the Meiji restoration. The area was the site of the Battle of Iwaki during the Boshin War. On April 1, 1889, the villages of Shinzan and Nagatsuka were created within Naraha District, Fukushima, which subsequently became Futaba District in April 1896. Shinzan was raised to town status on February 1, 1913. Shinzan merged with Nagatsuka on April 1, 1951 becoming the town of Shineha, which changed its name to Futaba on April 1, 1956.
Futaba was severely affected by the Fukushima Daiichi nuclear disaster, and the 2011 Tōhoku earthquake and tsunami on March 11, 2011. Besides sustaining considerable damage from the earthquake, and the tsunami (which devastated the coastal area), the town was evacuated en masse on the morning of March 12 as it is located well within the 20 kilometer exclusion radius around the damaged Fukushima Daiichi nuclear power plant On March 28, 2013, the central government rezoned the town into two areas according to different levels of radiation, with residents permitted to return to one of the zones for daytime visits, but would continue to be prohibited from entering the other zone due to dangerously high levels of radiation for at least another four years. However, the zone opened to daytime return of residents was only 4 percent of the town area, and the town remains uninhabitable.