Faculty of Medicine  Universitas Airlangga was developed with a wide range of challenges. Uncertain state conditions, lack of teaching staff, neglected space, and unclear status. But all the challenges were able to be overcome with enthusiasm and hard work. This historic period will be an important part in the footsteps of the Faculty of Medicine, Airlangga University (FM UNAIR). This is a challenging period. Along with the gloomy administration of the United Republic of Indonesia (RIS), FM UNAIR also experienced many difficulties..

April 1, 1950, Prof. G. M. Streef handed over the position of chair of Faculteit der Geneeskunde to Prof. Dr. M. Syaaf. During the Republican administration, the name Faculteit der Geneeskunde was changed to Faculty of Medicine in Jakarta and its branch of Faculty of Medicine Surabaya. Thus the Government of Indonesia has three (3) faculties of medicine, namely in Jakarta, Surabaya and Yogyakarta (the University of Gajah Mada including the Faculty of Medicine was established in 1949). Surabaya branch has just started their education and new students in level II, mostly from Faculteit der Geneeskunde. Surabaya is a top priority for the establishment of new universities. At that time, the Minister of Education, Muhammad Yamin, said that in Surabaya there were already several supporting facilities. In East Java there are several laboratories and have been the center of the investigation of the sugar and plantation industries which can be a supporting system for higher education institutions.

Surabaya is also the center of the development of the Eastern Indonesia Region. Surabaya is also the capital of East Java Province with a population of more than 18,000,000 (in 1954). Therefore, the establishment of universities in the city of Surabaya is a responsible action and fulfills the ideals of the East Java people and the Indonesian people. These ideals are: By ending the phase of the struggle to achieve and uphold independence, the struggle of the Indonesian Nation is now entering the stage of development implementation.

The historic day fell on Wednesday, November 10, 1954. President of the Republic of Indonesia Ir. Soekarno inaugurated the establishment of  Universitas Airlangga. Airlangga University was the first university established by the government after the dissolution of the United Republic of Indonesia (RIS) and the re-establishment of the Unitary State of the Republic of Indonesia (NKRI).  Its establishment is by combining branches of two different universities in Surabaya, namely the Faculty of Medicine and the Dental Institute branch of the Surabaya branch of the Universiteit van Indonesia which was established by the federal state, and the Faculty of Law branch of the Gadjah Mada University established by the Republican government. Earlier, it could be said that the establishment of Airlangga University was the union of two different institutions and had been politically at odds with each other. It can also be said that Airlangga University is a unifying university. It is this spirit of unity that President Soekarno wants to live in facing various challenges and changes.

Furthermore, FM UNAIR immediately established a faculty flag which was flown along with the flags of other faculties at Airlangga University in addition to the Red & White. The foundation of the establishment of Airlangga University was stated in  Government Regulation No. 57 of 1954, which took effect on November 10, 1954 and was established in Jakarta on November 1, 1954 by President Soekarno..

At April 1, 1955, Universitas Airlangga was separated from Jakarta & Yogyakarta, which was signed by the President of Airlangga University (A.G.Pringgodigdo), the President of the University of Indonesia (Bahder Djohan), and the President of Gadjah Mada University (M. Sardjito) on April 9, 1955 in Surabaya. The separation includes the surrender of the branch office of the university concerned with all equipment and lecture buildings, as well as the surrender of employees.

The Surabaya branch of the Faculty of Medicine, which was only separated from its parent Faculty of Medicine, Universitet Indonesia in 1954, was merged into Universitas Airlangga. Universitas Airlangga was born when Indonesia had just ended a long war and drained many resources. The return of Dutch troops to Indonesia was due to fierce resistance by the Indonesian people. As a result, various infrastructures have been damaged, the economy has stalled, political consolidation has experienced many disruptions. It has an impact on the existence of universities.

In 1959, another breakthrough was made by holding an affiliation with the University of California Medical Center in San Francisco from the United States. The affiliation contract was signed on July 8, 1959 in Washington, DC. The six-year affiliate contract is to improve the quality of doctor education and improve the quality of FM UNAIR teaching staff. During the affiliate program, 29 lecturers from the United States came to Surabaya and 89 FM UNAIR lecturers were sent to the University of Calfornia to deepen their respective fields of study. During the affiliate program, there were three ‘Chief of Party’ (United States chief of staff in Surabaya) namely Dr. W D. Forbus (1960 – 1962), Dr. William A. Reolly (1962 – 1963), and Dr. Donald L. Ferris (1963 – 1935).

Master Program of Basic Medical Science (BMS) was officially established in 1993, through the Dir Jen DIKTI Decree, No.593/DIKTI/Kep/1993, Ministry of Culture and Education R.I.

This Master Program was a new form the previous program which was already independent as a study program in each department. Until now Master Program has separated into many study programs, in both within FM UNAIR or in other Faculties in Universitas Airlangga. At FM UNAIR there are currently 5 study programs, one of which is Master Program of Basic Medical Science (BMS)