Minamishimabara is located about 60 km southeast of Nagasaki City (by land), and covers the area from the southeastern to southern tip of the Shimabara Peninsula.

Nagasaki Minamishimabara has a humid subtropical climate (Köppen:Cfa) with hot summers and cool winters.

The area was the site of considerable foreign trade and Portuguese and Spanish missionary activity, and by the early Edo period, a large percentage of the population were Kirishitan.

Due to misgovernment, high taxes and persecution of Christianity, the population rose in the Shimabara Rebellion of 1637, with the peasants occupying the fortress of Hara Castle as their strongpoint.

After the Meiji restoration, the villages of Katsusa, Kuchinotsu, Minami-Arima, Kita-Arima, Nishi-Arika, Higashi-Arima, Dozaki, Nutsu, and Fukae were established with the creation of the modern municipalities system on April 1, 1889.

The city of Minamishimabara was founded on March 31, 2006, from the merger of the towns of Arie, Fukae, Futsu, Kazusa, Kitaarima, Kuchinotsu, Minamiarima and Nishiarie (all from Minamitakaki District).

Minamishimabara has a mayor-council form of government with a directly elected mayor and a unicameral city council of 19 members.