[1] The total area of the city is 341.79 km2 (131.97 sq mi) Located in the central part of Nagasaki Prefecture, Isahaya is surrounded by the ocean on three sides and the Tara mounts to the north.

The biggest is the Isahaya Bay reclamation project (諫早湾干拓事業) by the Ministry of Agriculture, Forestry and Fisheries that started in 1989.

On September 1, 1940, it annexed the villages of Oguri, Ono, Yuki, Matsuyama, Motono, and Nagata to form the city of Isahaya.

[3] On March 1, 2005, the towns of Tarami, Moriyama, Iimori, Takaki and Konagai (all from Kitatakaki District) were merged to create the new and expanded city of Isahaya.

Isahaya has a mayor-council form of government with a directly elected mayor and a unicameral city council of 26 members.

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