During its liquidation, it turned out that the Faculty of Medicine, UII, Surakarta, found it difficult to break away from UII, not all of them accepted it. Many want to continue their studies as UII medical students. Finally, the leadership staff of the Surakarta Medical Faculty proposed to the board of waqf boards that the UII Medical Faculty be moved to Yogyakarta.
Until the end of 1974, the Medical Faculty of UII was still officially running. In 1975, because the facilities were still limited and especially because of a government regulation regarding the administration of private medical faculties, students who had already been accepted were transferred to the Sebelas Maret University (UNS) Surakarta Faculty of Medicine. Since then UII has no medical faculty.
Later in its development, driven by the desire to take part in improving health status, as well as the high demand for doctors in Indonesia, UII plans to open another medical faculty in the first decade of the 21st century. With a hard struggle, FK UII finally got permission to organize a medical education program based on the letter from the Director General of Higher Education Ministry of National Education no 3084/D/T/2001. Since September 3, 2001 the learning process has begun to be implemented at the Faculty of Medicine, UII.