The FEF was founded after the passing of Ezio Franceschini (1983) through the initiative of his sister and heir, Anna Maria Franceschini, Claudio Leonardi, his student, and some of his closest friends. Following a few years of informal activity, the FEF was officially established in Florence on 13 December 1987 by act of the notary Mario Piccinini. Among those present were founding members including Franceschini's sister Anna Maria, his friend Oscar Luigi Scalfaro, elected as President, his student Claudio Leonardi, named Director, and other friends - Giuseppe Cremascoli, Marcello Olivi and Giovanni Orlandi.

The founders formed the first Governing Board, and created a Board of Guarantors to bring together eminent figures from Italian culture and society (among these were Eugenio Garin, President of the Istituto Nazionale di Studi sul Rinascimento, and Giovanni Nencioni, President of the Accademia della Crusca), adding in 1998 a Scientific Committee to represent the main fields of research promoted by the Institute.

Under the presidency of Scalfaro, the FEF acquired legal personality (through the presidential act D.P.R. 17 April 1990) and was admitted to the list of organisations that the then-Ministry of Cultural and Environmental Heritage considered worthy of State support. After Scalfaro was elected President of the Republic of Italy in 1992, he left his position at the Foundation but was subsequently elected Honorary President of the FEF. Replacing him as president was Marcello Olivi, a lawyer from Padua and friend of Ezio Franceschini, who continued to lead the Foundation until his 81st birthday (2004). Claudio Leonardi, who up till that time had held the role of Director, then took up the reins. In 2008 the Foundation had a new president in Mario Piccinini, another member who had been involved with the FEF since its origins, and had served as part of the Board of Statutory Auditors.

In 1987, the library (containing around 16.000 books) and personal archives of Ezio Franceschini were moved to the Foundation's location in Florence, inside the Galluzzo Charterhouse. Over the course of time, thanks to bequests or acquisitions by the Foundation, collections of books and papers from other Medievalists have been added: first and foremost from Gianfranco Contini, but also from Vittore Branca, Tullio Gregory, Lorenzo Minio Paluello, Bruno Nardi, Aldo Rossi, José Ruysschaert, and most recently from Claudio Leonardi.

At the beginning, the main focus of the FEF was to bring greater accessibility to the important work of Ezio Franceschini through the conservation, study, and publication of papers, documents, correspondence and writings he had bequeathed. This mission grew broader over the years, to encompass the works of other scholars whose books and papers are now conserved by the FEF, giving rise to a centre for studies and for the promotion of cultural patrimony which is a significant and influential part of Italian and European history. Thanks to this activity, the FEF has been listed among the organisations that the Italian Ministry of Cultural Heritage and Activities considers worthy of State support since 18 May 1990.

The FEF was granted the status of nonprofit organisation (O.N.L.U.S.) on 30 January 1998.

Over time, the FEF widened its scope to include the promotion of research on medieval culture, studied by Ezio Franceschini, Gianfranco Contini and other scholars whose works are conserved by the FEF. In collaboration with SISMEL and with universities and research centres within and outside of Italy, the FEF has undertaken to provide, from its constitution, strong support and advancement of medieval studies (defined as spanning from the 6th to the 15th centuries and including literary production both in Latin and Romance languages). To achieve this objective, the FEF acts on many levels: supporting young scholars through grants for study and prizes for doctoral theses; organising projects, research teams, conferences and workshops; and rendering texts, manuscripts, and resources increasingly more available through the creation of databases. In recognition of these activities, the Italian government registered the FEF as an institute for scientific research, as defined by the decree of the prime minister D.P.C.M. 8 May 2007 and art. 1 para. 353 of the Law dated 23 December 2005, n. 266.

To complement its support of research, in 2001 the FEF launched together with SISMEL its postgraduate specialisation course in medieval Latin literature and philology. The Course is structured like a doctoral programme in research, and brings together professors from many Italian and European universities. The degree is equivalent to the Ph.D. granted by Italian universities, according to the ministerial decree D.M. 3 April 2001, published in the Official Gazette of the Italian Republic nº 104, 7 May 2001.

In 2011 the FEF was recognised for its role as institute for research on the Middle Ages by the Law of 23 September 2011, n. 169 (Concessione di contributi per il finanziamento della ricerca sulla storia e sulla cultura del medioevo italiano ed europeo), which starting from 2012 - 25 years from the inception of the FEF - will allow the Foundation to guarantee comprehensive support for all the activities of the institute.