In the context of the events of 17 November 1989, the students of our faculty, true to the sense of freedom and the tradition of democratic principles, established a strike committee at the faculty, organized a faculty-wide strike, and tried to gain the support of the workers of the East Bohemian Region factories in order to implement political changes. As a consequence of their action, personnel changes were made in the management of the Faculty of Medicine and some clinics.

In 1991-1992, rehabilitation doctorates were awarded to 17 students who had been expelled from their studies in previous years for political reasons.

In the 1992/1993 academic year, the Faculty of Medicine opened the study of general and dental medicine in English. From the academic year 1992/1993 to the end of 2019, 438 foreign students have graduated in general medicine and 111 foreign students have graduated in dentistry.

On 14 April 1992, the Scientific Council discussed and approved the "Regulations for Postgraduate Studies at the Faculty of Medicine in Hradec Králové" based on Act No. 172, Section 22 of 4 May 1990 on Higher Education. In the academic year 1992/93 the first postgraduate students started their studies. Between 1 January 1995 and 31 December 2019, a total of 404 students graduated and defended their PhD degrees, both in theoretical and clinical fields. Postgraduate doctoral studies were available in 18 disciplines. The new Higher Education Act of 1998 finally enacted the details of doctoral studies (including the accreditation of fields of study) and abolished the award of the rank of CSc. The Faculty of Medicine lost its full legal personality, acquired in 1990, and many of its competences began to be exercised directly by Charles University.

In 1993, the Bachelor of Nursing was opened. Between 1997 and 2019, 722 candidates defended their Bachelor's degree.

In 1995, the Faculty of Medicine celebrated its 50th anniversary. On this occasion, an exhibition on the activities of the Faculty since its foundation was held. The monograph Faculty of Medicine of Charles University in Hradec Kralove 1945-1995 was published. The President of the Republic Václav Havel sent a letter of greetings to the jubilee Faculty of Medicine. In the jubilee year, a total of 33 professional congresses, conferences and symposia were held in honour of the Faculty of Medicine.

On 6 May 1996, a purchase agreement was signed between the City of Hradec Králové, represented by the Mayor of the City Ing. Martin Dvořák and the Faculty of Medicine of Charles University in Hradec Králové represented by the Dean Assoc. Prof. MUDr. Karel Barták, CSc., according to which the Faculty of Medicine acquired the faculty building for a symbolic price of CZK 1.

In 1998, the faculty participated in an exhibition held on the occasion of the 650th anniversary of the foundation of Charles University.

In 2004, the 50th jubilee student scientific conference was held.

On 6 October 2015, the opening ceremony of the building of the Teaching and Research Centre of Charles University in Hradec Kralove took place, when the joint scientific and academic centre of the Faculty of Medicine and the Faculty of Pharmacy in Hradec Kralove was officially opened.