St. Francis Health Care Service was started in 1998 by Faustine Ngarambe (a former CSC novitiate), Ann Guloba (an HIV positive activist), Ruth Nabirye (a nurse), and 2 counselors – all local Ugandans. Ann Guloba died 2 years later. Having worked with the Jinja Diocese in the HIV/AIDS department as a social worker, Faustine realized that the HIV/AIDS pandemic was much bigger than a medical issue. Through the first funding (£10,000) from Mercury Phoenix Trust, a British charity, St. Francis rented a two-bedroom house and hired a motorcycle and a team of five volunteers. Every Monday morning a nurse would ride on a motor bike with a box of medicine to visit the bedridden for treatment of opportunistic infections and counselling. The next four years saw St. Francis expand into a much more spacious building to accommodate the growing number of clients and staff. A clinic was established to provide comprehensive treatment and care to the infected and affected population of Jinja and the surrounding districts. Realizing that HIV/AIDS had become more of a social problem than a medical one, St. Francis introduced a psychosocial arm to deal with the social needs of the clients and their dependents. Programs like education sponsorships, enterprise and skills trainings plus many other capacity building initiatives were started.

St. Francis currently provides a comprehensive and inclusive package of services including health, socio economic, and food security, child protection / youth empowerment and family strengthening for the populations in Buikwe and surrounding districts. St Francis Health Care Services found it necessary to expand its services that covered four Sub- Counties of Soroti District; namely Gweri, Katine, Tibur and Arapai with a population of over 66,000 people. But this Soroti branch later closed due to limited funding.