He was born to Pathan father Rasheeduddin Khan who was the became one of the founding professors of Jawaharlal Nehru University, where he taught Political Science and a Telugu Hindu mother Leela. He also has an elder sister.He is married to TV host Mini Mathur. They have two children Vivaan and Sairah.
Khan started his career at age 25 as a cinematographer for the Discovery Channel documentary film Beyond the Himalayas (1996) directed by Gautam Ghosh. He then made his own directorial debut with the documentary [The Forgotten Army] (1999) based on Subhas Chandra Bose's Indian National Army. He then directed two more documentaries before shifting his focus to mainstream cinema.
In November 2014, Khan was slated to start filming Bajrangi Bhaijaan featuring Salman Khan and Kareena Kapoor Khan. The film was released on 17 July 2015 during the Eid weekend. Reports have also surfaced of Khan signing Hrithik Roshan for a romantic film produced by Sajid Nadiadwala, which is scheduled to begin filming in July 2015.