Due to misgovernment, high taxes and persecution of Christianity, the population rose up during the Shimabara Rebellion of 1637, which was suppressed with extreme severity by the Tokugawa shogunate.

In more recent history, major eruptions in 1990–1991 resulted in pyroclastic flows, which killed 43 people and forced the temporary evacuation of hundreds of others.

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

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

Main crops include ice, radishes, carrots, potatoes, Chinese cabbage, small watermelons, mangoes, strawberries, pomelos, tobacco as well as chicken and cattle.

Shimabara is also a popular tourist destination, due to its historical associations, location in Unzen-Amakusa National Park, and numerous onsen.

The most popular tourist destination within the urban area is Shimabara Castle and the nearby "Samurai Street".