The house was handed over at a function attended by Chief Minister Mamata Banerjee, who is on a three-day visit to Darjeeling since May 14, and the Gorkha Janamukti Morcha President Bimal Gurung.
"The Ramakrishna Mission will take care of maintenance of the building," Banerjee said announcing Rs one crore from the state government for its renovation.
Banerjee said that the historic building would be made a heritage institution and would be used for the purpose of women's empowerment.
Roy Villa in Darjeeling is the house where Sister Nivedita died on 13 October, 1911.