He was the fourth son of Abu Sa'id Mirza, the emperor of the Timurid Empire in what is now Kazakhstan, Uzbekistan, Afghanistan, Tajikistan and eastern Iran.

His first wife and chief consort was Qutlugh Nigar Khanum, a princess of the Chagatai Khanate and daughter of Yunus Khan of Moghulistan.

[2] Umar Shaikh's mother was not explicitly named in any historical sources, including the Baburnama, his son Babur's autobiography.

However, Babur did refer multiple times to a certain Shah Sultan Begum (d. 1501) in a way that suggested she was Umar Shaikh's mother.

If this wording were interpreted to say that they were full brothers, this would mean that Shah Sultan Begum was mother to all three rulers, and thus the daughter of Aurdu-Bugha Tarkhan Arghun, who is known to have been Ahmad and Mahmud's maternal grandfather.