Zakir Hussain was born in Hyderabad, India, his ancestor Hussain Khan migrating from Kohat to Kaimganj, Farrukhabad, Uttar Pradesh, in 1715. His own family too migrated from Hyderabad to Kaimganj, where Hussain grew up. Hussain's father, Fida Hussain Khan, died when he was ten years old; his mother dying in 1911 when he was fourteen. He attended Islamia High School, Etawah, and was then educated at the Anglo-Muhammadan Oriental College, now Aligarh Muslim University, where he was a prominent student leader. He received his doctorate in economics from the University of Berlin in 1926.