The institute was established in 1999, after it was suggested by Ishfaq Ahmad, by the Government of Pakistan, led by the Prime Minister Nawaz Sharif. Its first director, who is designated as Salam Professor, was Dr. Ghulam Murtaza who was appointed in 1999. It also participated with the projects led by the Khan Research Laboratories (KRL) and the Pakistan Ministry of Science and Technology (MOST).