The establishment of the University of Muhammadiyah Semarang was initiated by the regional leadership of Muhammadiyah Central Java since 1996. The process was followed up by the establishment of the founding committee of the University of Muhammadiyah Semarang based on the decree of the regional leadership of Muhammadiyah Central Java number : SK.PW/III.B/9.6/001/1997.

With the preparation through intensive meetings, resulting in an agreement on the establishment of universities in the form of universities. On August 4, 1999, the Minister of Education and culture of the Republic of Indonesia issued the operating license of the University of Muhammadiyah Semarang with number : 139/D/O/1999.

Study programs that obtained operational licenses at the beginning of the opening in 1999 as many as 14 study programs include: Public Health Study Program (S.1), Statistical Studies Program (S.1), Mechanical Engineering Study Program (S.1), Mechanical Engineering Study Program (D.III), Electrical Engineering Study Program (S.1), Electrical Engineering Study Program (D.III), Food Technology Study Program (S.1), Agricultural Technology Study Program (S.1), Management Studies Program (S.1), Corporate Administration Study Program (D.III), accounting Study Program (D.III), English Study Program (S.1), English Study Program (.D.III), Japanese Language Study Program (D.III).

In its development in 2000, the Public Health Study Program (S.1 Cross Track), Mechanical Engineering Study Program (S.1 cross-track) in 2001, Nursing Studies Program (S.1) in 2002 and Nursing Studies Program (S.1 Cross Lane) in 2003.

Entering the second year in accordance with the mandate of the Tanwir session of the regional leadership of Muhammadiyah in Karanganyar, all Muhammadiyah universities in Semarang were merged into the University of Muhammadiyah Semarang (UNIMUS) which was then followed up with the issuance of the decree of the regional leadership of Muhammadiyah No. III.B / 1.A/087 / 2001.

Administratively, the merger with the Academy of Nursing, Nutrition Academy and health analyst academic was carried out starting in 2002, and officially the merger obtained the decree of the Minister of National Education with No. 28/D/O / 2005 so that the existing courses increase nursing courses (D.III), Nutrition study program (D.III), Health Analyst study program (D.III).

Academic year 2006/2007 UNIMUS opened a new study Program, namely the Study Program D.III Midwifery with operational permit number: 2294/D/T / 2006. in the academic year 2008/2009 has opened a new study program, namely S-1 Accounting (SK.Higher education number 2092 / D/T / 2008); S-1 Medical Education (SK. Dikti number 2940/D/T / 2008); nurse profession Program ( SK. Higher education No. 267/D/O / 2008); S-1 Mathematics Education (SK.Higher education number 1040/D/T / 2009); S1 – English Language Education (SK.Higher education number 1271 / D/T / 2009); D.IV health analyst (SK.Dikti number 1941/D/T / 2009) and S1 Nutrition Science (SK.Higher education number 218/D/O / 2010).

Until 2011, the University of Muhammadiyah Semarang had 22 study programs consisting of 11 Strata 1 programs, 1 Diploma IV Study Program, 7 Diploma III study programs and 1 Professional Program.