In the early 19th century due to the political upheavals in Europe the seed of liberalism sprouted in the Philippines. On January 1, 1820 a royal decree was issued which authorized the creation of a nautical school upon the recommendation by the consulate of commerce. Gov. General Mariano Fernandez Folgueras issued a decree on February 11, 1820 establishing the ESCUELA NAUTICA DE MANILA. It was inaugurated on April 05, 1820 and wad formally opened for classes on the same day. The building was located inside Intramuros, near Cuartel de Espana.

The course of study was headed by Admiral Gabriel Ciscar and the academic instruction conformed with the naval course study.

The Board and Tribunal of Commerce administered the school with powers to prescribe entry qualifications and to decide on administrations . After the abolition of the board and tribunal , the state assumed the full control of the Nautical School , and was administered through the Commandant General of the Cavite Naval Station. Revision of administration rules was affected in 1893. In 1860, a new curriculum was introduced as a result of the industrial revolution.

In the earthquake of June 03, 1863 many buildings were destroyed in Intramuros , and the Escuela did not escape destruction. It was transferred to another government building , until the coming of the Americans.

During the revolution in 1898, the Escuela was temporarily suspended but many of it's graduates joined the forces of General Emilio Aguinaldo. ( The first flag officer commanding the Navy of the Revolution was General Pascual Ledesma from Negros, alunmus of the Escuela ).

On December 15, 1899 , the school was reopened by the Americans and named , the Nautical School of the Philippines Islands. The Superintendent was U.S Navy Commander Cottman who was relieved by Lt. George Cooper on December 25, 1899. First instruction was conducted inside the Cuartel de Neisie on December 15, 1899, retaining Spanish as the medium of instruction with English , as an additional subject.

In January 1900, the school was transferred to an old Spanish-type bodega on Calle Sta. Elena in San Nicolas district which was improvised by the U.S Navy .It was in the building where the school was temporarily closed by the civil government in 1907.

Upon representations made by the Philippine Shipowners Association, the Nautical school was reopened again in 1913.

The Civil government thought it wise to conduct nautical education as a unit of Philippine School of Arts and Trades now the Technological University of the Philippines. The nautical unit was ideally located by the Pasig River on Arriceros, but instruction was entirely left to the Filipino officers. One of the first graduates of 1916 was Col. Rafael Ramos of the PC who was hand-picked by President Quezon to organize the offshore patrol. It was then renamed Philippine Nautical School with the Commonwealth regime.

On October 31, 1939, It was placed under the office of the Defense Secretary until the war. During the battle of Bataan, many of its graduates participated in the defense of the country.

The Japanese regime the Philippines did not close the Philippine Nautical School. Rather it was expanded into a bigger establishment that included not only the training of the nautical officers but also of the marine engineers and ordinary seamen.

After the war, the school was placed under the administrative control of the Commander of the Phil. Naval Patrol. But during the term of President Quirino economic experts convinced the President that the Philippine Nautical school is much needed by the merchant marine, and therefore should be returned to the Department of Education. The school was placed under the vocational division of the Bureau of Public Schools , Department of Education.

Then in 1962 , a study was conducted to look into the various phases of technical and technological education. With the result of this study , R. A. No. 3680 was approved converting the Philippine Nautical School ( which was located in Robert St. Pasay City ) into PHILIPPINE MERCHANT MARINE ACADEMY which was placed under the Department of Trade and Industry , in June 1963.

In January 1968, It was transferred to its present site in Fort Andres Bonifacio, Makati City, making it the only maritime school on top of the hill.

With the introduction of new technology in the shipping industry in the mid 70's, the Academy has to adopt new technology, In 1982 with the help of International Maritime Organization (IMO), the rehabilitation of the Academy's curriculum and facilities were effected. This was to conform with requirements being implemented by the IMO.

Today , the Philippine Merchant Marine Academy is the most modern and the most updated maritime school among members of the ASEAN countries.