In 1897, Naval Museum was established under the name of “The Museum and Library Administration Office” in a small building in the Imperial Dockyard with Sultan Abdülhamit II’s permission and Minister of Navy Bozcaadalı Hasan Hüsnü Pasha’s orders. The museum served in various buildings regarding the conditions of that time. Finally, in 1961, the Museum was moved to a building in Beşiktaş (which was previously served as the Treasury) and began to serve here under the name of “The Naval Museum and Archive Directorate”.

Storage near this building which was built in the 20th century and had been previously used as aircraft shed, repair workshop and garage was assigned for the Museum. The historical boats collection consisting of the galley and the imperial caiques was transferred to this building and this collection was opened to public in “The Gallery of Historical Caiques” in 1971.

As the building which served as the Gallery of Historical Caiques was actually designed as a depot, the museum staff encountered some problems in preserving and displaying the collection. In order to overcome these obstacles, it was decided to build a new museum building in the available area. In this context, a national architectural design competition was organized on 14 August 2005. In 2008, the award-winning architectural design was chosen to be built as the new museum building.

Finally, the construction of the new museum building consisting of the annex exhibition building, the gallery of historical caiques, the cultural center and the open exhibition area began according to the modern museology concept. First of all, a temporary depot was built in order to preserve the historical caiques during the construction period. In 2009, the caiques were transferred to this depot.

When the renovation/restoration process of the Naval Museum completed in September 2013, the collection of historical caiques was transferred to this building. The new museum began to welcome its visitors on 4 October 2013.