Faculty of Pharmacy, Universitas Gadjah Mada, was founded by the Indonesian Ministry of Health on September 27, 1946 under the name Perguruan Tinggi Ahli Obat (PTAO) or College of Medicine Expert (The date is set as the birthday of Faculty of Pharmacy). This college became a member in a joint-college consisting of the College of Medicine, College of Dentistry, College of Agriculture, and College of Veterinary Medicine, all chaired by Prof. Dr. M. Sardjito and domiciled in Tegalyoso Hospital Complex, Klaten District. At the time of the incident of Indonesian Communist Party’s rebellion and the 2nd military action by the Dutch army, then on December 19, 1948 the college was forced to discontinue its academic activities. A large number of faculty members and students at that time joined the Indonesian army to participate in the guerrilla or the Red Cross team.

After the Roem-Van Royen agreement on May 7, 1949, there was an idea that the college should be reactivated. On May 20, 1949, a meeting of the College Committee was held at the Kepatihan Hall. Prof. Dr. M. Sardjito as the Chairman of the joint-college located in Klaten District agreed to reconstruct the planned college – he then asked for a place in Yogyakarta Sultanate. With the permission as well as the generosity of Sri Sultan Hamengkubuwono IX, several buildings belonging to the Sultan’s Palace such as Mangkubumen could be used for the college activities.

Due to the great assistance from the Vice President Drs. Moh. Hatta, Minister of Education and Culture Ki Mangun Sarkoro, Minister of Health Dr. Soerono and Prof. Soetopo, Minister of Finance Lukman Hakim, Minister of Transportation and Public Works Ir. Laoh and Ir. Sitompul, Minister of Welfare and Agriculture I.J. Kamiso and Sadjarwo SH along with the Secretary-Generals Mr. Hadi, Ir. Putuhena and Ir. Goenoeng, the college reopened on November 1, 1949. At that time, there had been already several colleges including College of Engineering and the School of Law owned by the Balai Perguruan Tinggi Gadjah Foundation in Yogyakarta, and each was still under the control of the related ministries. Then, there was an idea that the existing Colleges and Schools were merged to be a university under the Ministry of Education and Culture (PP&K). The idea was implemented by the opening of the State University of Gadjah Mada (UNGM) by the Ministry of Education and Culture on December 19, 1949 (now designated as the birthday of Universitas Gadjah Mada).

Meanwhile, the College of Medicine, College of Dentistry and College of Pharmacy were still under the control of the Ministry of Health. Through the Government Regulation No. 37 PP Year 1950 dated August 14, 1950, signed by Mr. Assat as the Temporary President, Ki Mangun Sarkoro as the Minister of Education and Culture and KRT. E. Pringgodigdo as the Minister of Justice, the Government of Indonesia confirmed that UNGM was under the control of the Ministry of Education and Culture. The term Perguruan Tinggi (college) was then converted into Fakultit, i.e. Fakultit of Medicine, Fakultit of Dentistry, and Fakultit of Pharmacy. In 1954, the Government decided to change the terms universitit and fakultit into Universitas and Fakultas. The Balai Perguruan Tinggi Gadjah Mada Foundation as a private institution did not longer exist so that UNGM was converted into UGM.

In the Propaeduese level (level I), class activities of the Faculty of Medicine, Dentistry, and Pharmacy (FKKGF) were still joined, with the same academic staffs but different exam questions. In the later development, that joint-faculty was broken down into three different faculties, i.e. Faculty of Pharmacy in December 19, 1955 based on the letter of instruction of the Minister of Education and Culture No. 53759/-Kab and Faculty of Dentistry in December 29, 1960 based on the letter of instruction of the Minister of Education and Culture No. 1090741/UU. Although those faculties were separated from each other, the academic activities were still organized in the same building (Mangkubumen), so during that time, the students of the three faculties were known as MAMACONGA (Student Society of Ngasem Complex).

Having separated from FKKGF, Faculty of Pharmacy still had no permanent faculty members yet; therefore, the management was taken by the temporary ones. The first Dean was Prof. Drs. R. Sardjono (from the Faculty of Medicine) and the secretary was Prof. Ir. Gembong Soetoto Tjitrosoepomo (from the Faculty of Agriculture). Since 1963, Faculty of Pharmacy began to have permanent faculty members.

In the early time of their establishments, faculties of UGM were dispersed all over Yogyakarta area; afterwards, Sri Sultan Hamengkubuwono IX gave some lands in Bulaksumur, Sekip and Karangmalang area for the establishment of a university. Soon after, the faculties were moved gradually to the new location. In 1968, Faculty of Pharmacy was moved to Karangmalang along with Faculty of Dentistry, Faculty of Medicine (Department of Pharmacology and Physiology), and Faculty of Cultural Sciences. In 1973, Faculty of Pharmacy occupied a new location in Sekip Utara until now. At that time, Faculty of Pharmacy still lacked faculty members earning pharmacist degree so the academic activities of doctoral level (the last level of undergraduate program) were conducted in Yogyakarta and pharmacist level were still being conducted in the city of Semarang. Since 1976, all of the teaching and learning processes in Faculty of Pharmacy have been performed in Sekip Utara campus, Yogyakarta.