The Naval Academy had been collecting literary materials on Chungmugong Yi Sun-shin since its foundation on January 17, 1946 and temporarily operated literature exhibition room within the library to publicly display them.

Since then, the Naval Academy Museum was founded and opened on January 17, 1976 in commemoration of the 30th anniversary of the Naval Academy. However, it was a simple expansion of the former exhibition room of Chungmugong Yi Sun-shin literatures. The Naval Academy Museum, at the time of opening in 1976, borrowed and used portion of the library building with the size not larger than a small office.

Then, the Museum reconstructed the Turtle Ship, which Chungmugong Yi Sun-shin invented, in its original size, and moored at the wharf used for distinguished guests of the Naval Academy on January 31, 1980 for exhibition. In February 23, 1981, a new independent Museum building was constructed at the current location of the Naval Academy Peninsula. In addition, expansion construction of the Museum was completed on April 28, 1990 to the present state of the Museum.