Jesuits first arrived on the African continent in the 16th Century under the direction of Saint Ignatius himself, and travelled to present day Ethiopia. Wherever they have gone, they have established social works, namely educational institutions and refugee services among others. The Society of Jesus in Eastern Africa was formally established in 1986. The Sudan, Ethiopia, Kenya, Tanzania and Uganda were joined under one superior and called the Eastern Africa Province of the Society of Jesus.

The Jesuits of this province planned to have a Secondary school in each of the five countries. The first Jesuit secondary school was established in the Sudan at Wau in 1985. Then Loyola High school in Tanzania took shape from 1989 when the late Fr. Louis Plamondon, S.J. was appointed to organise the building project. Loyola High School admitted first students in Pre-Form One in 1995. Building the school at Mabibo was designed to serve mostly the needs of the local Mabibo population. The Jesuits wished to offer quality education for those with the ambition to study but are not able to afford such an education.

Gonzaga Preparatory and Primary School is the brain child of Loyola High School. When Loyola High School was cerebrating its 10th anniversary in 2005, one of the events which were planned was to start a community service program. The community service program started as a way of marking the 10th anniversary of Loyola High School. The community service program takes Loyola students to various places where they rendered their services. One of these places where students were rendering service was the Sara cobet orphanage center which was run by Mr. Lihangwike Komba. Through community service, Loyola High School students could offer their services to many children who are orphans and disadvantaged in the area of Mabibo.

In 2005, Mr. Patrick Doherty, his wife Mrs. Maureen Doherty, their daughter Siobhan Doherty, accompanied by Fr. Joe Daoust, SJ and other friends from Our Lady Queen of Peace Foundation, Inc. Canada came to visit the Jesuits working in Dar es salaam and Dodoma. Seeing the misery of children who were at the orphan center where Loyola Students were doing their community service, the family decided to enter into partnership with the Jesuits to help more the orphans and other disadvantaged children from the area of Mabibo and its neighbourhood. The idea of building Gonzaga Preparatory and Primary school started from this partnership between the Jesuit and Our Lady Queen of Peace Foundation. The building of Gonzaga Preparatory and Primary School was completed in January 2008 and the first intake started on 14th January 2008 with about 200 students from Pre-Standard One to Standard Three. Most of these students came from the Orphans Centers and other students were transferred from other Primary Schools. However there was a special class of Standard Five from the orphans who came from Sara Cobet and SOS International.