After the start of the national isolation policy, the Tokugawa Bakufu banned Christianity from 1614 and replaced Arima Naozumi with Matsukura Shigemasa.

Matsukura, who strictly enforced the prohibition against Christianity with mass executions, also severely raised taxes to pay for the construction of his new Shimabara Castle from 1618-1624.

It was the seat of the local government until 1871, when the former Shimabara Domain was merged into the new Nagasaki prefecture.

A number of the yagura were restored in 1960 and 1972, and the keep was rebuilt in 1964 in reinforced concrete as a city museum containing exhibits of the Kirishitan culture, Shimabara Rebellion and feudal period.

In 1980, a memorial museum was opened in honor of Seibo Kitamura, a noted sculptor.