The school was founded in 1946 by the Mill Hill Missionary Fathers when the administration of the Budini College decided to transfer the institution to a site with easy access to social amenities.

They moved to occupy the premises which had been vacated by the Franciscan Sisters. Fr. Mc Gough became the first head teacher of the new institution now named Jinja College. Initially, a private junior school (S.1 to S.3) became a government aided school and upgraded to secondary status (S.1 to S.4) in 1965 with Fr. Jone Jones as its head teacher. In 1981, the school was up graded again to A’ Level status (S.1–S.6), offering Arts and Science courses (subjects) with Mr. Boniface Kategano as the Head teacher.

The following have ever headed the school Mr. Ogutti Bichachi (1984-1996), Ag. Head teacher Mr. Oryema Anthony (1996)    Mr. Iisat Ignatius (1997-2001) and Mr. Kawuki Joseph (2001-2013)