The area of Takachiho was part of ancient Hyūga Province. It features prominently in Japanese mythology as the land where Ninigi descended from the heavens, sent by Amaterasu, the sun goddess. It contains the Ama-no-Iwato shrine which is, according to myth, the location of the cave where Amaterasu hid until Ame-no-Uzume lured her out. From the late Heian period into the Sengoku period, the area was controlled by the Kikuchi clan, which was associated with Aso Shrine in Higo Province. The area later was contested between the Shimazu clan of Satsuma Province and the Otomo clan of Bungo Province. After the establishment of the Tokugawa shogunate, it was part of the holdings of Nobeoka Domain. The village of Takachiho within Nishiusuki District, Miyazaki was established on April 1, 1889 with the creation of the modern municipalities system. Takachiho was raised to town status on April 1, 1920. Around 1920, arsenopyrite was mined in the northern part of the town, and the production of arsenite supported the town's economy until the mine was closed in 1962. On September 30, 1956 Takachiho annexed the neighboring towns of Iwato and Tahara, followed by the town of Ueno April 1, 1969.

During World War Two, the 2nd Raiding Brigade trained in the town and were sometimes known as the Takachiho paratroopers.[1]