Khan scored the highest amongst his pupils on his matriculation exam, and subsequently received an admission—sponsored by National Conference leader Maulana Masoodi—to Sri Pratap College in Srinagar. Around this time, the Partition of British India had taken place, and the princely state of Jammu and Kashmir was divided by a United Nations Security Council-mandated ceasefire line that ended the First Kashmir War between the newly-independent states of India and Pakistan. The area Khan was living in was now administered by India, whereas the princely state's western districts and entire northern region (including his birthplace of Astore) had come under Pakistani control. Sheikh Abdullah, a Kashmiri politician, became the first elected Prime Minister of Jammu and Kashmir. Despite his admiration of Abdullah, Khan was a staunch supporter of Pakistan and favoured its right to exercise sovereignty over all of Kashmir. When Khan held a protest after the assassination of Pakistani Prime Minister Liaquat Ali Khan, he was forced to leave the Indian-administered state, leading him to migrate to Pakistan in January 1952. He attempted to get into Garden College in Rawalpindi, but was refused admission on the grounds that his former college in Jammu and Kashmir was not recognized there. He subsequently enrolled in Edwards College in Peshawar but was soon expelled due to trouble with the college principal. Finally, he enrolled in Sindh Madressatul Islam University in Karachi and graduated in 1957, obtaining a degree in law in 1962.