The organization of Muhammadiyah which submissive in da’wah through education and health field, need health workers, especially doctors to perform health care institutions that spread out thorough Indonesia. For that reason, the Head of Muhammadiyah organization established Faculty of Medicine UMY in March 1993. Along with the others health workers demand from the citizens, Nursing program established in 2000, dentistry program established in 2002, and Pharmacy program in 2010. With these varieties of program studies, Faculty of Medicine UMY changed its name into Faculty of Medicine and Health Science, and Medicine program managed under the management of Faculty of Medicine and Health Science since 2010.

In 2002, Medicine program of Faculty of Medicine and Health Science has been accredited by National Accreditation Agency for Higher Education of The Indonesian Ministry of Education Directorate General of Higher Education with the qualification of B. In 2015, Medicine Program obtained another accreditation from Independent Accreditation Institution for Health Higher Education. Based on the latest accreditation result, Undergraduate Medicine Program classified as B accreditation, meanwhile Doctor Profession Master Program achieved A accreditation

There are a lot of variety of grant programs that helped the development of Faculty of Medicine and Faculty of Medicine and Health Science, which are A2 Competition of Grant Program from Ministry of Research, K1 Inherent Grant for the development of technology of information and Competition of Medicine Department Quality Improvement Grant Program in 2011-2013 obtained from World Bank-DIKTI.