Colegio de San Juan de Letran emerged from the fusion of two similar institutions both located in Intramuros. 

The first was founded in 1620 by Don Juan Geronimo Guerrero, a retired Spanish Officer, who transformed his hermitage home into an orphanage called the Colegio de Niños Huerfanos de San Juan de Letran. Its purpose was to educate and mold orphans into good Christian citizens. 

At about the same time, another institution by the name of Colegio de Huerfanos de San Pedro y San Pablo was established by the Dominican brother Diego de Santa Maria at the Convent of Santo Domingo. The founders of these two institutions with identical origin and purpose did not only share a common concern for the children of Intramuros but they were also linked by strong bonds of friendship. It was not surprising therefore that their institutions were merged into one even in their lifetime in 1630 and became known simply as the Colegio de San Juan de Letran.

The name San Juan de Letran was inspired from the major basilica of Saint John Lateran in Rome, mother of all Christian churches. Early in the history of the College, its chapel was granted many of the privileges enjoyed by the major Basilica. Saint John the Baptist for whom the Basilica is named, is also the patron saint of the College.

In 1690, Letran was declared as an ecclesiastical college. In 1738, six scholarships were granted by the King of Spain for Chinese, Japanese, and Tongkinese (Vietnamese) students. St. Vicente Liem de la Paz was among the students who enjoyed this scholarship.

A royal decree of May 1865 pronounced Letran as a College of the First Class. The school’s curriculum was reviewed and revised according to European and American patterns in 1886. Further expansion took place in 1894 and adjustments were made with the arrival of the Americans in 1900.

In 1937, a three-storey building replaced the old structure. The growth of the Colegio was temporarily arrested when the building was bombed in 1941 and then turned into a garrison by the Japanese army in 1944. The Colegio was temporarily housed in the Dominican church and convent of San Juan del Monte. After the war in 1946, Letran returned to its home in Intramuros.

In a span of more than three centuries, Letran produced alumni who became the builders of the Filipino nation. The names of Manuel Quezon, Sergio Osmena, Apolinario Mabini, Marcelo del Pilar, Padre Mariano Gomez, Francisco Baltazar, Emilio Aguinaldo, and many others are enshrined in the hearts of every Filipino. 

Colegio de San Juan de Letran has faithfully lived up to her mission. No revolution nor earthquakes, no world war nor man-made disasters have broken or changed the resolve of our Dominican administrators to continue this noble task of providing excellent christian education. Countless great men have passed and will continue to pass through the portals of this old venerable institution - revolutionaries, heroes and patriots, presidents, leader of the church and most notable of all, a saint. In its long history, there will always be the successes as well as challenges for Letran. But for years and generations beyond, in the end, Letran will remain standing as a cut above the rest - proud of its heritage and sure of the time - honored and enshrined ideals of DEUS, PATRIA, LETRAN.