St. John's College began in the year 1887 in Belize City. In 1922 the College was moved to an area outside the city known as Loyola Park. The 1931 hurricane destroyed the college and once again it was brought back to the heart of Belize City - the Holy Redeemer compound. There it remained for twenty years. In the late months of 1952, a new site and new buildings formed a new St. John's College about one mile to the north of the city. Today this site is commonly known as Landivar, named after the Central American poet and renowned scholar, Rafael Landivar, S.J.

Early in 1952, a two-year program of post-secondary education called, in the British tradition, Sixth Form, was inaugurated. The program led to the Advanced Level Examinations set by Cambridge University. Three students made up the first class of the Sixth Form, which was under the direction of Fr. Robert Raszkowski, S.J. The program grew slowly during the first ten-year period. The Sixth Form students used the same classrooms and library as the secondary school students. During this period, St. John's College was granted the status of an advanced-level ("A"-Level) school by Cambridge University.

The Sixth Form program at St. John's changed dramatically in 1964. The secondary schools in the various districts of the country now had graduates ready for advanced level work. St. Catherine Academy in Belize City elected to combine their program with St. John's College. Yearly enrolments grew, and continued to grow. The Sixth Form was then moved across campus to a nearby classroom building and a new science laboratory, and it began to develop its own library.

In an effort to provide wider opportunities for further education for graduates of the Sixth Form, St. John's College in the mid-1960s broadened the program of studies so that it met the requirements of the Associate Degree awarded by junior and community colleges in the United States. In effect this enabled graduates of St. John's College Sixth Form to enroll in baccalaureate degree programs in US colleges and universities.

In 1996 the Board of Trustees of St. John's College voted to change the name of the Sixth Form to St. John's College Junior College in recognition of the fact that a tertiary institution has developed over the last thirty years which had long exceeded its "Sixth Form" origins.