Zainab Sultan Begum was born a Timurid princess and was the fifth daughter of Sultan Mahmud Mirza, who was Babur's paternal uncle.
Zainab's paternal uncles included Umar Sheikh Mirza, the ruler of Ferghana Valley, who later became her father-in-law as well while her first cousins included her future husband, Babur, and his elder sister, Khanzada Begum.