Nafisa Ali was born in Kolkata, the daughter of Ahmed Ali, a Bengali Muslim, by his wife Philomena Torresan, a Roman Catholic of Anglo-Indian heritage. Nafisa's paternal grandfather, S. Wajid Ali, was a prominent Bengali writer. Her paternal aunt (father's sister) was Zaib-un-Nissa Hamidullah, a Pakistani journalist and feminist. Nafisa is also related to the decorated Bangladeshi freedom fighter and soldier Bir Pratik Akhtar Ahmed. Nafisa's mother is now settled in Australia.

Nafisa went to Sr. Cambridge from La Martiniere Calcutta. She has also studied Vedanta taught by Swami Chinmayananda, who started the center Chinmaya Mission of World Understanding.