The body of the victim was found gagged, tied up and with three stab wounds at the Green Oaks home in the village of Montferrier-sur-Lez near Montpellier.
French Catholic bishops' conference spokesman, Olivier Ribadeau Dumas, tweeted condolences for the woman after police were called to the scene on Thursday night.
More than 100 security service personnel were called to the African Missions Society-operated premises after a member of staff - not the stabbing victim - rang police to report being attacked.
The identity and motive of the perpetrator, who was armed with a shotgun and a knife, remains unclear but security at religious and other sites in France has been stepped up following a string of Islamic extremist attacks recently.
Islamic State group attacks on Paris in November 2015 left 130 dead, 84 died after a lorry rampage in Nice on 14th July 2016 and Father Jacques Hamel was killed at his Catholic church in Normandy twelve days later.
French police have said they don't believe this incident near Montpellier is terror-related.