The library embryo already existed on August 1, 1982, which was located at Jl. K.H.Ahmad Dahlan Yogyakarta. Then in 1984 the UMY library moved to the Jl. H.O.S. Cokroaminata No 17 Wirobrajan Yogyakarta at the same time with the moving of the Muhammadiyah University Yogyakarta / UMY campus. 

Simultaneously the UMY campus moved from Wirobrajan to the new campus to Jl. Lingkar Selatan Tamantirta Kasihan Bantul Yogyakarta dated July 1, 1997, then the embryo of the library, officially became the UMY Library with the Decree of the UMY Chancellor Number 090 / SK UMY / VII / 1997 occupying the A.R. Fachruddin A 1st floor.

Then on July 19, 2000, the UMY Library moved to a new building, namely Building D, 2nd floor and 3rd floor. Until September 2019, the 2nd floor was used for public reading rooms, canteens, American Corner, French Stalls, prayer rooms, Taiwan Education Center, repository rooms & journal. 3rd floor for the collection of printed books, study room, prayer room, Muhammadiyah Corner, processing room, internet room, warehouse. Meanwhile, the 1st floor is for administration, prayer room, assembly room 1 & 2, carrel room, Muhammadiyah Corner, and knowledge sharing room.

Besides the Central Library, there are also Postgraduate libraries, Faculty of Medicine and Health Sciences, Faculty of Engineering, Faculty of Islamic Religion, Faculty of Agriculture, Faculty of Law, Faculty of Social and Political Sciences, Faculty of Economics and Business, Institute of Islamic Practice and Development (LPPI) and Language Training Center library which all have integrated management, procurement, services, procurement of books, and e-journals, budget, and human resource assignments.