Nagasaki Prefecture contains the following Historic Sites of Japan.
As of 27 January 2025, thirty-four Sites have been designated as being of national significance (including three *Special Historic Sites).
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| align="center"|Shimabara Castle Site<br><br><small>Shimabara-jà  ato</small> || Shimabara || || || || || |- | align="center"|Koshitaka Site<br><br><small>Koshitaka iseki</small> || Tsushima || || || || || |-
As of 1 May 2024, ninety-five Sites have been designated as being of prefectural importance.
As of 1 May 2024, a further three hundred and twenty-three Sites have been designated as being of municipal importance.