Khan’s father, Mir Taj Mohammed Khan, was an Indian independence activist from Peshawar who campaigned alongside the Khudai Khidmatgar, a nonviolent resistance movement led by Abdul Ghaffar Khan that sought a united and independent India.^[3][4] Mir was a follower of Abdul Ghaffar Khan,^[5] and affiliated with the Indian National Congress.^[6] He was also the cousin of the major general in the Indian National Army Shah Nawaz Khan.^[d] According to Khan his paternal grandfather, Mir Jan Muhammad Khan, was an ethnic Pashtun (Pathan) from Afghanistan.^[9][6][10] However, his paternal cousins in Peshawar later clarified that the family speaks Hindko and is originally from Kashmir, from where they settled in Peshawar centuries back, contradicting the claim that his grandfather was a Pashtun from Afghanistan.^[6][11] As of 2010, Khan’s paternal family was still living in the Shah Wali Qataal area of Peshawar’s Qissa Khwani Bazaar.^[6]

In 1946, Mir moved to Delhi to study law at Delhi University.^[12] When the partition of India occurred in 1947, he was forced to stay in Delhi, and did not return to Peshawar until many years later.^[13] Khan’s mother, Lateef Fatima, a magistrate, was the daughter of a senior government engineer.^[14][d][15] His parents were married in 1959.^[16]