The history of Kumamoto Prefecture has been documented from paleolithic times to the present. Kumamoto Prefecture is the eastern half of Hinokuni (meaning "land of fire"), and corresponds to what was once called Higo Province. Exceptions are the part of Kuma District, which had once been part of Sagara Domain, and Nagashima which was included in Kagoshima Prefecture.

Kumamoto Prefecture is roughly divided into three areas, namely, the northern area with Kikuchi River, Shirakawa River and Mount Aso Area; the Kumagawa Area including the Hitoyoshi Basin and the Amakusa Island Area. The first one is the Kumamoto han, and the second the Hitoyoshi han and the third one is the Amakusa Area, once controlled by the Tokugawa shogunate. The history of Kumamoto is characterized by kofuns in natural beauties or volcanic activities, the ritsuryō and the following rise of samurais, the arrival of Katō Kiyomasa from Nagoya, wars around the Bakumatsu including the Satsuma Rebellion, and public problems concerning Minamata disease. After the establishment of the Yamato Government or Yamato Ouken, the history of Kumamoto has been constantly under the influence of the Central Government.

About one-third of the archaeological sites of the Lower Paleolithic age in Japan were found in Kumamoto Prefecture. A few of these have been excavated. Mainly these were in the outer Aso mountain areas and Kuma district. The oldest one is the Ishinomoto Site in Hirayama machi in Kumamoto City; dating back more than 30,000 years ago by the radiocarbon dating method. A large number of artifacts or stone tools such as stone axes and knives were excavated, suggesting that Kyūshū was inhabited by a number of hunter-gatherer societies.

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