In 1990, the establishment of the Faculty of Medicine in Jember was initiated with a proposal for the Medical Education Study Program, which received support from the Governor of the First Level Regional Head of East Java and a positive response from the Governor of the First Level Regional Head in Eastern Indonesia, namely NTB, NTT, and East Timor.

In 1997, a Faculty of Health Development Workshop was held at the University of Jember, led by Prof. Dr. Ma’rifin Husin, Chairman of the Health Sciences Consortium. This marked the beginning of a new era in preparing for the establishment of the program. It was followed by several workshops on curriculum development, hospital readiness, collaboration with the Faculty of Medicine at Airlangga University in Surabaya, and partnerships with district hospitals around Jember, including Lumajang, Bondowoso, Situbondo, and Banyuwangi. This journey concluded with a visit to the Health Discipline Commission on December 27, 1999, in the context of launching the Medical Education Study Program.

On April 27, 2000, a decree was issued by the Director-General of Higher Education at the Ministry of National Education of the Republic of Indonesia, numbered 120 / Dikti / Kep / 2000, regarding the establishment of the S-1 Medical Education Study Program at Jember University, with Prof. Dr. Soenarjo as the program head. On January 2, 2003, RSUD dr. Soebandi Jember was inaugurated by the Minister of Health R.I. as a Type B Teaching Hospital, serving as a “Teaching Hospital” for the Medical Education Study Program at Jember University.

Since June 19, 2006, a decree numbered 4557/J25/PP.9/2006 has been issued, officially establishing the Faculty of Medicine at the University of Jember, with the first dean being Dr. Wasis Prajitno, Sp.OG. According to the Decree of the National Accreditation Board for Higher Education for Study Programs with valid operational licenses from the Ministry of National Education and other Ministries, numbered 008 / BAN-PT / Ak-XIV / S1 / VI / 2011, dated June 23, 2011, the Faculty of Medicine at the University of Jember was accredited with a B rating.

This achievement was further recognized in 2016 when the faculty received accreditation from the Independent Accreditation Institute for Health Universities (LAM-PTKes) with the predicate “Accreditation A.” This remarkable accreditation was reaffirmed in 2022 with the predicate “Superior Accreditation,” as indicated in SK Number 0418/LAM-PTKes/Akr/Sar/VI/2022 for the Medical Education Study Program and SK Number 0418/LAM-PTKes/Akr/Pro/VI/2022 for the Medical Professional Study Program. Additionally, in 2023, FK UNEJ received another special gift with ASIIN International Accreditation.