The Muhammadiyah Organization that focus on da’wah in the field of education and health, needed health staff, especially doctors to activate the health service institution of Muhammadiyah. For this reason, in March 1993, The Central Leadership of Muhammadiyah established Faculty of Medicine UMY to educate doctors candidate. With the increasing of the need of other health services in the society, Nursing Study Program established in 2000, Dentistry Study Program in 2002, and Pharmacy Study Program in 2010. With the variety of the Study Programs, Faculty of Medicine UMY changed its name into Faculty of Medicine and Health Science, and Medicine Study Program included under the management of FKIK UMY in 2010.

In 2002, the Medicine Study Program achieved accreditation from National Accreditation Institution for Higher Education (BAN PT) The Ministry of Education and Culture with accredited B classification. In 2015, this faculty achieved another accreditation from Independent Accreditation Institute for Health Higher Education (LAM-PTKes). Based on these two accreditation results, Medicine Study Program (Bachelor Degree) has B Accredited Classification, meanwhile the Doctor Profession Study Program (Master Degree) has A Accredited Classification.

Various grant programs helped the development of both FK and FKIK UMY, some of them are A2 Competition Grant Program from Dikti, Inherent K1 Grant for the development of information technology and The Competition of Medicine Study Quality Improvement Grant (PHK PKPD) in 2011-2013 achieved from World Bank-DIKTI.