The institute was built on an open lot that since the start of the World War I had been used for coastal artillery training.

The Higher Naval Engineer Institute in Sevastopol was established in 1951 on the resolution of the Council of Ministers of the Soviet Union.

In 2014, after the Annexation of Crimea by the Russian Federation, some of Academy's faculty and students were transferred to Odesa continuing instruction and their education at the Naval Faculty of the Odesa National Maritime Academy (Maritime College of Technical Fleet).

At the same time, the name of the Sevastopol institution was restored as the Black Sea Red Banner Higher Naval School "Admiral Pavel Nakhimov", functioning again as a Russian Navy officer commissioning educational institution.

On September 1, 2022, by decree of the President of the Russian Federation, the school was awarded the Order of Nakhimov.