The school was founded by the Catholic Diocese of Díli in 1983–84,[clarification needed] when East Timor was still part of Indonesia.

[2] The history of the school begins with an initiative by the Indonesian government of occupation, to enlist the support of Catholic traditionalists groups in Timor, so that, by allowing the founding of a school, it opens a channel of dialogue with the main support group for the insurgent organizations CNRM and FRETILIN.

Having been forced to close its doors in 1992, on charges of subversion, in 1993 Bishop Dom Ximenes Belo transferred the administration of the São José Day School to the Society of Jesus, as a maneuver for the institution to return to work.

[4] On August 26, 1999, in an impromptu assembly, Father Joseph Ageng Marwata announced that the São José Day School would be closed indefinitely owing to "unexpected events".

[2] In 2000, reflecting the political change brought about by UNTAET's mandate, the school resumed its activities, but with a reduced number of students and teachers.