The Faculty of Science was established with the creation of the University of Girona through the agreement with the Catalan Parliament published in the Official Gazette on 31 December 1991. Prior to this, Girona relied on the Universitat Autònoma de Barcelona, which started in 1970 with 98 students. The department was recognised in 1972 as the University College of Girona’s Sciences Section and was integrated into the Universitat Autònoma de Barcelona in 1982, with 207 students and 27 teaching staff. In 1989 the creation of Estudi de Ciències science department was approved within the framework of the Estudi General de Girona. During 1989-1990, there were 418 enrolled students and pre-EHEA Biology and Chemistry degrees were taught. These pre-EHEA degrees were the ones being taught when the University of Girona was created in 1991. The curriculum for the pre-EHEA degrees in Biology and Chemistry were adapted the and the curriculum for Environmental Studies launched during the academic year 1993-94, with the latter becoming official in 1995. The process for setting up the bachelor's degree studies which have now replaced the former pre-EHEA degrees began during the Academic year 2009-10. The change to bachelor's degree studies triggered the start of a new study, that of Biotechnology, supplementing the Faculty of Sciences’ offered studies. Two dual bachelor's degrees in Biology-Biotechnology and Biology-Environmental Sciences have also been offered since the academic year 2012-13, which, together with the four master’s agrees, in Molecular Biology and Biomedicine,  Environmental Change, Advanced Catalysis and Molecular Modelling, Science and Technology of Waters Resources and Applied Chromatographic Techniques and doctoral studies, make up the centre's range of educational offers. Some 1400 students have been taking their university studies the Faculty of Sciences every year.

The Faculty of Sciences is also the headquarters of three departments (Biology, Environmental Sciences and Chemical Sciences) and the departmental unit of the Chemical Engineering and Environmental Laboratory at the Department of Chemical and Agricultural Engineering and Agrifood Technology, and accommodates three research institutes (IEA, IMA and IQCC) and four chairs managing the work of 24 research groups.

The Faculty initially used the rooms that the Science Department of the Estudi General de Girona occupied in the Casa de Cultura, later expanding to other locations in Albereda street (Fórum building) in Girona city centre. In February 1997 it moved to new headquarters on the Montilivi Campus, the location of the Faculty to this day. The Faculty of Sciences’ main building was originally 7,399.14 m² in overall area, with an extra 1,994 m² from an extension to Part3 (total area: 9,393 m²) and a later extension, in year 2009, with the educational spaces of the Common Lecture Theatre, shared with the Polytechnic School, up to a total of 11,475 m². Its total area is currently 12,899 m², since the extra 1424 m² added from the Common Lecturer Theatre’s extension in June 2015, with the research part where most of the Biology Department was located.

The first dean of the Faculty of Science was Dr Lluís Polo, who was nominated as Chair of the University Management Commission in 1992. At that time the Faculty called itself the Faculty of Experimental and Health Sciences.  As Faculty of Experimental Sciences, the first elections for dean were won by Josep Enric Llebot, who was later replaced by Dr Carles Pla. The Faculty adopted its definitive name: The Faculty of Science. Dr David Brusi was dean during the transfer to the current headquarters on the Montilivi Campus and until October 2003. After a brief transition period in which Dr Joan Miró and Dr Margarida Casadevall served as acting deans, Dr Manel Poch was chosen as dean. Later, from 2006 until 2008, Dr Crisanto Gómez and Dr Juan M. Sánchez occupied the post of dean. Dr Victòria Salvadó was elected as dean for two terms, from 2008 to December 2016, followed by Dr Jesús Colprim until November 2022 and subsequently by Dr Crisanto Gómez. Dr Mònica Iglesias Juncà has been dean since June 2023.

_{Updated in June 2023}