He was born in Moyobamba, province of San Martín, on January 16, 1861. His parents were Augusto San Martín and Martina Peña. When he was very young, his parents sent him to the Preparatory School of the Navy, in Callao, which he entered in February 1876.
He was as an aspirant in the monitor "Atahualpa" when beginning the war with Chile in 1879. He was promoted to Guardiamarina in November of that year. In 1880 was part of the endowment of the boat "Independencia", commanded by the Second Lieutenant Jose Gálvez; Aboard the aforementioned boat attended the operations against the blockade that the Chileans had imposed on the port of Callao.
His glorious action will take place during the early hours of May 25 of that year. Together with the commander José Miguel Galvez and the medicine practitioner Manuel Ugarte, they fought with the "Janequeo", an enemy boat that surpassed them in size and walk, supported in turn by the boat "Guacolda". The armament they had on board had been rendered unfit for their misfortune, they had to go to the "Janequeo" and lift a bomb that they threw on the boat, causing it to explode with gunfire. Both boats, the "Independence" and "Janequeo" sank, and in this action Emilio San Martin will perish without its body could be recovered.