This Prestigious Medical Institution came into existence in the remote corner of Agriculture University, Lyallpur in 1973-74. Faisalabad Medical University(previously Punjab Medical College Faisalabad started its journey all alone under the enthusiastic supervision of Late Prof. Dr. M. H. Toosy in very hard circumstances and lack of facilities. Initially District Headquarter Hospital was upgraded to 551 bed strength and was affiliated for teaching and learning purpose. The College building was completed by 1981-82 under the leadership of 2nd Principal late Dr. F.M. Choudhry, thus enabling the shifting of all the basic department to the new site in March, 1982. All departments are modern with well equipped independent lecture hall, with audio visual facilities, laboratories, museums, demonstration rooms and offices for the teaching staff.
Allied Hospital (1100 beds) was established in 1978. It was equipped with the state of art machinery and new technology for teaching as well as healing purpose with courtesy of JICA (The Japan Government). The institute is recognized by General Medical Council Britain and Irish Medical Council Republic of Ireland. The Government of Punjab granted antonomy to this institution in 1998 and a Board of Governors was empowered to run the institution. In 2002 Government of Punjab revised the act. New Emergency department has been setup at DHQ and Allied Hospital and 100% free medicines were provided to all patients for first 24 hours.
A computer Research and Resources Lab was established in 2004 with the cooperation of Higher Education Commission through University of Health Sciences, Lahore. This research center connects the teachers and students with all international libraries online, provided that the world is a global Village. FMU, Dental Section started its first batch in 2009. A new medical emergency block has been established with the help of philanthropists. The Dental Section of FMU was recognition by PMDC in 2014.
On 5th May 2017, college was reconstituted and upgraded as a university for purpose of imparting better medical education, encouraging and arranging extensive research and publication in the field of medical science, holding examinations and awarding medical degree and for ancillary matters. Prof. Dr. Al Fareed Zafar was appointed as first Vice Chancellor of the university.
Prof. Dr. Zafar Ali Choudary (T.I) is the 2nd Vice Chancellor of the University. Today college is one of the most beautiful worth seeing institutions with lush green lawns, beautiful landscape, blossoming flowers and above all dedicated students and teachers.