The Missionaries of Charity (MC) established in 1950 by Mother Teresa will be head by German-born Sister Mary Prema.
"It is now officially announced that Sister M Prema is the new superior general," MC spokesperson Sister Christie said on Wednesday.
The new superior-general replaces Sister Nirmala who was elected for the third-time but refused to lead citing ill health and a desire to live a contemplative life in the congregation.
Sister Nirmala was recently awarded the Padma Vibhushan, India's second highest civilian honour, recognising her service to the poor and downtrodden.
According to sources, the election took place during the congregation's general chapter in Calcutta, where 163 sisters of whom 74 are of Indian origin voted for Sister Prema.
The Missionaries of Charity have 19 homes in Kolkata alone which include homes for women, for orphaned children, and for the dying; an AIDS hospice, a school for street children, and a leper colony.
The 62-year-old Catholic religious order consists of over 4,500 sisters and is active in 133 countries.