In a quick response to the desire of Fayoum citizens and their political leaders, as well as the wide spread of diseases, namely schistosomiasis, renal failure, hepatitis, diseases of the urinary tract and digestive system and fever, Cairo University Council agreed on March 30, 1994 upon establishing a branch of Faculty of Kasr El Aini in Fayoum.

Once informed, the Committee for Medical Studies Sector, the Supreme Council of Universities (SCU), formed a committee to evaluate establishing a faculty of medicine in Fayoum affiliated to Cairo University. On February 17, 1994, the committee paid a visit to Fayoum Governorate to examine Fayoum hospitals; the committee recommended benefiting from Fayoum Public Hospital and other related hospitals to be a teaching hospital for the faculty.

In its session on February 9, 1995, the committee approved of establishing a faculty in Fayoum; also, the Supreme Council of Universities (SCU) expressed its approval in its session on May 7, 1995 of:

* establishing a branch of Faculty of Medicine, Kasr El Aini, Fayoum Branch
*The academic year 1995/1996 witnessed the beginning of study at this department with 50 students; the study was temporary at Faculty of Medicine, Kasr El Aini, Cairo University, until completing the buildings of Faculty of Medicine, Cairo University, Fayoum branch.

* Thus, the study began since the academic year 95/1996 temporarily at faculty of medicine, Kasr El Aini, through Admission Office and a special stamp. In order to start the study at the faculty in Fayoum, the former president of Cairo University approved on September 25, 1997 of starting the study at the faculty headquarter since the second term in February where the students of the first and second classes attended regularly; most of them were from Fayoum, while the students of the third class were left to complete their study at Faculty of Medicine, Kasr el-Eni until having a teaching hospital devoted to the faculty in Fayoum. In its session on July 31, 1996, Cairo University Council approved of the independence of the faculty branch in Fayoum to be an independent Faculty of Medicine. The issue was referred to the Supreme Council of Universities where the Committee for Medical Studies Sector expressed its approval on October 31, 1996, because of having the following ingredients:

*on April 6, 1998 Fayoum Governor agreed upon making Nafisa El Hosry Hospital be a teaching hospital, and the amendments needed to be a teaching hospital were made with a capacity of 80 beds and was inaugurated on March 24, 1999

* The Minister of Health issued his two decrees Nos. (20, 73) of 1998 by virtue of Fayoum Faculty of Medicine had the privilege of making use of all Fayoum hospitals in teaching and training the faculty students and doctors. An agreement was signed with the Ministry of Health allowing the faculty students and doctors to train and study in all hospitals affiliated to the ministry in Fayoum

* The old university building was altered to be a hospital with a capacity of 60 beds; it was called the University Teaching Hospital. For engineering considerations, the building was evacuated; so the other clinical specializations were inserted in Nafisa El Hosary Teaching Hospital.

* Prof. Dr. Galal M. Said, President of Fayoum University, gave his orders concerning rehabilitating the building of Exam Hall (Faculty of Engineering, annex building) to be a teaching hospital as a transitional stage until equipping the new teaching hospital.

* The Republican decree no. 193 of 2005 was issued to announce the independence of Fayoum Faculty of Medicine from the Kasr El Aini School of Medicine.