Established in between 1964-1970 during Prof.Dr.Sardjito serving a period as a Rector, Universitas Islam Indonesia developed rapidly both in the hub and the regions around Indonesia. The university began to inaugurate exact sciences faculties. One of them is the UII Medical School located in Surakarta. The Medical School was established on 9 December 1964, initiated by Prof. Dr. Sardjito, Prof KHA Kahar Muzakir, Dr. Soekiman Wijosandjojo and KH Imam Ghazali.

In 1967, the Director General of Higher Education issued an order No.164 of 1967 regarding the “Requirements of Private University Management”, to be set out particularly in a written instruction issued by the Head of Private University Bureau and the Official of the Directorate General of Higher Education No.1223/PT/III/1968 on 3 December 1968. The order resulted on the disseverance of UII long nurtured regional branches. Some of the regional branches are gone through dismissal soon after transferring their prospective students to UII main campus in Yogyakarta, while the rest of them are transforming into a new private university or consolidate to a local university sharing a similar branch of knowledge. Similarly what happened to UII Medical School at Surakarta which then consolidated with Universitas Sebelas Maret Medical School (UNS) Surakarta.

UII Medical School Surakarta has a hard time to adjust their condition post the dismissal. Many of the students are eager to continue their study as part of UII Medical student. This has caused the leader of the Medical School Surakarta to offer a notion of translocating the UII Faculty of Medicine to Yogyakarta.

The Medical School of UII was officially run until the late of 197, however in 1975 due to lack of supportive facilities and mainly because of the government policy on the management of the private medical school, every prospective student is assigned to Universitas Sebelas Maret Medical School (UNS) Surakarta. Since then UII no longer maintains Faculty of Medicine.

Subsequently motivated to improve Indonesian health care and fulfill the high demands of doctors, UII set up a goal to reestablish their Faculty of Medicine during the first decade of 21st century. All the efforts finally paid when UII granted the permission to reestablish their Faculty of Medicine through the letter of Director General of Higher Education Ministry of Education No. 3084/D/T/2001. Hence, since 3 September 2001 the UII Faculty of Medicine recommences their learning activity.