Franciscan missionary activity in Uganda began when Fr Marcin Zagórski arrived on 13 April, 2001. Fr Marcin had previously worked in Zambia.

The mission was officially established on 1 August, 2001, when Fr Bogusław Dąbrowski arrived. Joining the mission in December was Fr Jarosław Wysoczański, followed by other brothers: Fr Lucjan Szczepański, Fr Piotr Tymko, Fr Marek Warzecha and Br Piotr Gorący. The missionaries began their work in the Diocese of Kasana-Luweero, in the village of Kakooge. Before they constructed their own monastery and finished construction on the parish church in Kakooge (a project begun by the previous parish priest), the friars enjoyed the hospitality of the mission of the Brothers of the Christian Schools (FSC).


On 3 January, 2010, the bishop created a new parish in Matugga, entrusting it to the care of the Franciscans. Work in Matugga was begun by Frs Marian Gołąb and Fr Szymon Majcherczyk; they were later joined by Fr Wojciech Ulman and in 2011 by Fr Adam Klag. Initially, the friars lived in a house provided by parishioners, but at the beginning of May 2010, they had already started construction on a primary school and a friary. The brothers moved into their new home on 6 December, 2011, and by Easter 2012, the school building was almost completely finished. Because there was no church in the new parish, Masses and other services are held in the school chapel. Construction of the parish church began on 3 March, 2013, and the brothers in Matugga are currently collecting funds to finish the church building. The parish also has seven so-called ‘access chapels’ dispersed over a 15km-radius from the parish centre. 


Another important date in the history of the Ugandan missions is 13 October, 2013, when the Franciscans of the Cracow province arrived at the Shrine of the Martyrs of Munyonyo in the district of Kampala, to begin work there.