On the retirement of Professor Salimuzzaman Siddiqui F.R.S. as Chairman PCSIR, his services were taken up by the University of Karachi and a "Postgraduate Institute of Chemistry" was established under his Directorship in 1966 in a wing of the Department of Chemistry. PCSIR provided the services of some of its staff (including Dr. Viqar Uddin Ahmad and Dr. Zafar H. Zaidi) and furniture during the initial phase of the establishment of this institute.

A generous donation was offered to the University for the Institute by the leading philanthropist/industrialist Mr. Latif Ebrahim Jamal H.I. on behalf of the Husein Ebrahim Jamal Foundation in 1976, the largest donation at that time in the history of the country. The Institute was accordingly named as "Husein Ebrahim Jamal Research Institute of Chemistry", in the memory of late Mr. Husein Ebrahim Jamal a leading industrialist and philanthropist.

Dr. Atta-ur-Rahman F.R.S. joined the Institute in March 1969 after obtaining Ph.D. from the Kings College, Cambridge University, later he accepted a 4-year assignment as a Fellow of Kings College, Cambridge University. He was then sent by Cambridge University to the University of Karachi during 1971-74 to assist in the setting up of a modern postgraduate institute of chemistry, and he brought with him donations of gas chromatograph, balances and a combustion microanalyser from Cambridge University. Dr. Atta-ur-Rahman succeeded in obtaining grants to acquire a new mass and NMR spectrometers, both of which were installed in 1973, within a year of his return to Pakistan. He was appointed as the Co-Director in 1977. He succeeded in winning several major projects for the institute from the West, which have transformed the institute into the finest center in Asia and one of the best in the world in the field of Natural Product Chemistry. He was appointed as the Director in January 1990, while Professor Viqar Uddin Ahmad took over as Co-Director in 1990. In 2000, Professor Bina S. Siddiqui was appointed as the Co-Director on the retirement of Professor Ahmad.

Molecular medicine is an emerging new field, which deals with the understanding of the molecular basis of diseases and then developing appropriate strategies for their early diagnosis, management and elimination. Knowledge of human biology and disease mechanism at molecular level is the most important step in developing effective disease prevention and treatment. In the year 2004, the Panjwani Center for Molecular Medicine and Drug Research (PCMD) was established through a generous donation and patronage of Ms. Nadira Panjwani H.I., S.I. (Chairperson, Dr. Panjwani Memorial Trust) in the memory of her beloved father, Dr. Mohammad Hussain Panjwani, a leading scholar and philanthropist. The main objective of the center is to train highly qualified manpower in the emerging new fields of molecular medicine and drug development. The academicians, clinicians and pharmaceutical researchers are brought together to translate basic scientific discoveries into new therapies, vaccines and diagnostic tests.

The efforts of Professor Dr. Dr. W. Voelter H.P., S.P. of Tuebingen University, Germany, deserve a special praise since the initial grant of 2.3 million DM, and later several other grants from the Republic of Germany were largely due to his untiring efforts, and collaborative researches continue with his group till today. Late Mr. Latif Ebrahim Jamal H.I., Chairman Ebrahim Jamal Foundation, continuing his patronage to the Institute, established the Latif Ebrahim Jamal H.I. National Science Information Center in 2005. The beautiful building of this one of the largest paperless libraries of the region was constructed under the direct supervision of Mr. Aziz Latif Jamal S.I. (Current Chairman Husein Ebrahim Jamal Foundation), able and committed son of (Late) Mr. Latif Ebrahim Jamal.

In 2002 Professor Dr. M. Iqbal Choudhary H.I., S.I., T.I. was given the responsibilities of the Director (Acting) of ICCBS and Co-Director of Dr. Panjwani Center for Molecular Medicine and Drug Research. In September 2008, he was appointed as the Director of the ICCBS institutions. During last fifteen years under his leadership, the institute has gone through a rapid and unprecedented expansion, both in terms of infrastructure development and academic programs, while maintaining the highest quality in research and student training. He obtained several large development grants from the government of Pakistan for a rapid, yet planned,expansion of the ICCBS.

The center has organized a number of major international conferences and symposia on various aspects of Natural Product Chemistry, Molecular Medicine, Spectroscopy and Protein Chemistry. The center had the distinction of hosting the 19th IUPAC Symposium on Natural Product Chemistry in January 1994 in which over 500 scientists from 52 countries, including 4 Nobel Laureates participated. Additionally the Institute has also been selected as one of the three library centers of the The World Academy of Sciences (TWAS). The center has been designated as the W.H.O. Center for Pesticide Analysis for the Eastern Mediterranean Region. The center is also a member of the IUCN-International, WAITRO, COMSATS and UNESCO. More recently the institute is designated as the OIC Center of Excellence in Chemical Sciences.

In 2001, the H.E.J. Research Institute and Dr. Panjwani center became a constituent institution of the International Center for Chemical Sciences (later named as International Center for Chemical and Biological Sciences (ICCBS)

In August 2003, an Industrial Analytical Center was established as the service wing of H.E.J. Institute. Third World Center (TWC) Laboratory complex was formally inaugurated by the Prime Minister of Pakistan in 2005 as an extension of the H.E.J. Research Institute of Chemistry. The building of TWC was renamed as Prof. Atta-ur-Rahman Laboratories by the Executive Board in 2011, in recognition of the outstanding services of Prof. Atta-ur-Rahman (FRS) who is now serving the ICCBS institution as the Patron-in-chief.

In 2004, the ICCBS received the most prestigious IDB (Islamic Development Bank) prize for the best science institution in the entire Islamic world. Recently, the IDB awarded the best science institution again to the ICCBS (second time), an unprecedented honor to any science institution in OIC region.