The Beacon Academy was founded in 2009 by architect Leandro Locsin Jr., son of the late National Artist of the Philippines for Architecture Leandro Locsin, and his wife Mailin Paterno-Locsin. The school was established to serve as the high school extension of its sister school, the Beacon School, located along Chino Roces Avenue in Taguig. According to Locsin Jr., the Beacon Academy aimed to continue the Beacon School's success of providing an internationally recognized curriculum that would provide Filipino parents an option for their children to maximize their potential as national and global citizens. Locsin added that its establishment was also a response to the rise of international schools in the country aiming to do the same. The school's campus opened in August 2010. Education Secretary Armin Luistro and Biñan Mayor Marlyn Alonte-Naguiat were among the guests of honor during the school's opening rites. Locsin Jr. currently serves as the Beacon Academy's board chairman.
