It was built during the 18th century to replace a smaller battery (called El Boquerón) that stood at the easternmost end of the San Juan islet.

Then-Governor of Puerto Rico Field Marshal Don Ramón de Castro y Gutiérrez, a brilliant strategist, prevented the British from advancing and frustrated their conquest of San Juan.

As recent as the year 2006, attempts were being made by the Instituto de Cultura Puertorriqueña and the U.S. Army Corps of Engineers to build a breakwater to stop any further deterioration from irreparably damaging the centuries-old fort.

[citation needed] In July 2007, the Fort was the scene of protests against the construction of a tourist project called Paseo Caribe that would block access to the fortification.

[3] After two decades closed to the public, in 2018 the Asociación Amigos del Fortín de San Jerónimo was created, a non-profit association that is responsible for the preservation and future reopening for the charity of the Puerto Rican people and tourists.