Chowdhuri was born in Kolkata to a family of Zamindars. Her father, Banku Behari Chowdhuri, was a doctor. Her mother, Urmila Devi, practiced Brahmo Samaj, which held the belief that young women should be allowed to go to school. By marrying Urmila, Banku was converted to Brahmo and outcast from Hindu circles. Many of the Chowdhuri children (apart from the second daughter who died early on) went on to become highly educated. Chowdhuri was the middle child of her five siblings, with one brother. Her aunt, Nirmala Devi, was married to Sir Nilratan Sircar. Her sister, Roma Chowdhuri, went on to become a teacher at Brahmo Balika Shikshalaya.