In 1979 he got a degree in Philosophy and Literature, Section of Modern and Contemporary History, at the University of Barcelona, with the thesis entitled "The MLE (Spanish Libertarian Movement) and its development in Catalonia (1939-1945)", directed by Josep Termes.
In 1993 he earned a doctorate at the same university with the thesis (in Catalan) titled "The History of Catalonia in the Primary and Secondary School (1975-1990)", directed by Pelai Pagès.
He renewed his charge as General Director of Research during the first months of the second tripartite government, while Josep Huguet was Counselor of the Department of Innovation, Universities and Enterprise.
Aside from these initiatives he also made possible the work of prominent researchers in Catalonia, such as Joan Massagué, Manuel Perucho or Juan Carlos Izpisúa.
He did research on textbooks and has also generated models for Primary and Secondary School based on the interaction between image and text, which have been widely replicated since the end of the 20th century to the present day.
Hernández has also collaborated in the development of new types of educational materials based on the design of books of activities which integrate documentation and learning resources.
In this sense, he conducted his doctoral thesis on the image of Catalonia in textbooks during post-Franco age: "La Història de Catalunya a l'ensenyament primari i secundari (1975-1990)".
He has developed several works of innovation and research focused on the importance of didactic iconography in history, and has applied the results in the preparation of social dissemination and textbooks.
He started his activities in museography in 1992, working on the project of partial restoration of the Iberian Citadel of Calafell (Tarragona), inspired by the educational experience of Lejre (Denmark).
The work explained the siege of Barcelona and stands as a model in museography by its modern conception, by the success of visitors, by the variety of museological strategies used, and also because of a quick design and implementation at low cost.
He has directed several doctoral theses on aspects of history, heritage, museology and didactics (Dr. Josep Antoni Serra, Dr. Rafael Sospedra, Dr. Andreu Besolí, Dr. Ismael Almazán, Dr. Xavier Rubio, Dr. David Íñiguez and Dr. Pilar Molina).
He has carried out field activities to identify specific areas of the battlefield and also participated in civic campaigns in defense of the integrity of the mountains of Pàndols and Cavalls (Tarragona).
He was author to the first attempt to write an Management Plan of the Historical Landscapes of the battle of the Ebro promoted by the Ministry of Territorial Policy and Public Works of the Generalitat de Catalunya.
Of special interest was the recovery and publication of the inventory of the Vapor Vell de Sants in the year 1847, a crucial document to better understand the process of industrialization in Barcelona.
Francesc Xavier Hernández has propugned the possibility of Ildefonso Cerdà as a designer of a new city as the capital of a new country, based on the Kabbalah, in the context of the rise of the Catalan Freemasonry during the 19th century.
His contribution was relevant in the campaign in defense of the Vapor Vell de Sants, which was emblematic as it marked the beginning of the recovery of the industrial heritage in Catalonia.
At the same time he provided the funds to start the excavation of mass graves in Catalonia, which was neutralized by the Memorial Democràtic and the Vice President of the Catalan Government environment.
Some of the archaeological campaigns in which he participated between 2003 and 2011, involving the recovery of bodies of soldiers (Albinyana, Gandesa, Castellbisbal, La Fatarella) were disabled or sabotaged by the Generalitat.