[10]: 566 [11][12][13] After completing his matriculation in 1942 in Kasur, Khan enrolled at the Government College University in Lahore and was a contemporary of Abdus Salam— the Nobel Laureate in Physics in 1978.

: 79 [20] In 1953, Khan left his graduate studies in physics at the Illinois Institute of Technology when he accepted to be a participant in the Atoms for Peace policy of the United States and started his training program in nuclear engineering offered by the North Carolina State University in cooperation with the Argonne National Laboratory in Illinois in 1953.

The six-factor equations for determining the multiplication of a nuclear chain reaction in a non-infinite medium.After graduating from North Carolina State University (NCSU) in 1953, Khan found employment with Allis-Chalmers in Wisconsin before joining the Commonwealth Edison company in Illinois.

[18] At both engineering firms, Khan worked on power generation equipment such as generators and mechanical pumps and participated in a federal contract awarded to Commonwealth Edison to design and construct the Experimental Breeder Reactor I (EBR-I) which built up his interests in practical applications of physics that led him to attend the Illinois Institute of Technology, and to attend the training program in nuclear engineering offered by NCSU.

[26][16][22][14] Khan was also known to have gained expertise in producing isotopic reactor-grade plutonium, deriving it from neutron capture, that is frequently found alongside the uranium-235 (U235) civilian reactors, in the form of low enriched uranium.

[29] In 1964 and 1971, Khan served as scientific secretary to the third and fourth United Nations International Geneva Conferences on the Peaceful Uses of Atomic Energy.

: 105 [32][33] The IAEA eventually entrusted Khan to oversee the construction of the ICTP in 1967, and played an instrumental role in establishing the annual summer conference on science in 1976 on Salam's advice.

[37] After his visit to the Bhabha Atomic Research Centre in Trombay as part of the IAEA inspection in 1964 and the second war with India in 1965, Khan became increasingly concerned about politics and international affairs.

[47][7] Khan played a crucial role in keeping grid operations running for the Karachi Nuclear Power Plant after its chief scientist, Wazed Miah, had his security clearance revoked, and was forced to migrate to Bangladesh.

[46] In 1982, Khan expanded the scope of nuclear technology for harnessing the agriculture and food irradiation process by establishing the Nuclear Institute for Food and Agriculture (NIAB) in Peshawar while moving PAEC's scope towards medical physics research by securing federal funding for various cancer research hospitals in Pakistan in 1983–91.

: 38 [51] Upon learning the news, Khan returned to Pakistan from Austria, landing in Quetta to initially attend the winter session to meet with PAEC's scientists before being flown to Multan.

[55] Although Khan was not a doctorate holder,[56] his extensive experience as a nuclear engineer at the reactor physics division at IAEA enabled him to direct senior scientists working under him on classified projects.

: 157 [58] Salam, who saw this program as an opportunity to ensure federal government's interest and funding to promote scientific activities in his country, took over the TPG's directorship with Khan assisting in the solutions for fast neutron calculations and binding energy measurements of the atomic bomb.

Ensuring the Corps would handle its part in the atomic bomb project, Khan requested the construction of the Metallurgical Laboratory (ML) near the Pakistan Ordnance Factories in Wah.

[61]: 41–43 [63] Eventually, the project was relocated to the ML with Qureshi and Zaman moving their staff and machine shops from the Institute of Nuclear Science and Technology with assistance from the military.

[27]: 60–61 [64][65] In 1975, Khan, in discussion with the Corps of Engineers, had selected the mountain ranges in Balochistan for the isolation needed to maintain security and secrecy.

[27] Scouting for a test site in 1976, the team searched for a high altitude and rocky granite mountain that would be suitable to take more than ~40 kn of nuclear blast yield, ultimately candidating the remote, isolated, and unpopulated ranges at Chagai, Kala-Chitta, Kharan, and Kirana in 1977–78.

[66][67] Preparations for the tests and engineering calculations were validated by Khan with Ahmad leading the team of scientists; other invitees to witness the test included Ghulam Ishaq Khan, Major-General Michael O'Brian from the Pakistan Air Force (PAF), General K. M. Arif, Chief of Army Staff at that time, and other senior military officers.

[66] Khan recalled to his biographer, decades later, that while witnessing the test: In 1977–80, the PAEC completed the designs of the iron-steel tunnels in Chagai region.

: 231–235 [71] By 1979, Khan removed PAEC's role in defense production moving the Wah Group, that designed the tactical nuclear weapons in 1986, from ML to KRL, and also founded the National Defence Complex (NDC) in 1991.

[72] The message was delivered to the Indian Prime Minister's Office, and the Non-Nuclear Aggression Agreement treaty was signed to prevent nuclear accidents and accidental detonations between India and Pakistan in 1987.

[73] In 1990, Khan advised the Benazir's administration to entered in negotiation with France over construction of nuclear power plant in Chashma.

[8] In 1976, Khan moved the Reactor School in Islamabad, renaming it as "Centre for Nuclear Studies (CNS)" and took the professorship in physics, as an unpaid part-time employment, alongside Dr.

[8] After his retirement from PAEC in 1991, Khan went to academia when he joined the faculty at the center for nuclear studies as a full-time professor to teach courses on physics while continuing to push for the CNS to be granted as university by the Higher Education Commission.

[27] As a scientist, Khan is remembered by his peers as brilliant researcher and engaging teacher, the founder of applied physics in Pakistan.

[35] During the Cold war, scientists became involved in military research on unprecedented degree, because of the threat communism from Afghanistan and Indian integration posed to Pakistan, scientists volunteered in great numbers both for technological and organizational assistance to Pakistan's efforts that resulted in powerful tools such as laser science, the proximity fuse and operations research.

[58] As a cultured and intellectual physicist who became a disciplined military organizer, Khan represented the shift away from the idea that scientists had their "head in the clouds" and that knowledge on such previously esoteric subjects as the composition of the atomic nucleus had no "real-world" applications .