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.