In 1992 the foundations for the Jan Perner Transport Faculty establishment were laid within the then Institute of Chemical Technology in Pardubice. There, on 1st October, the Department of Transport was established. The department consisted of two professors, two associate professors and a senior lecturer. Only a month later intensive preparations for opening of an independent faculty were started. Detailed study documentation was created and a provision of personnel for pedagogical, scientific, administrative and technical activities of the Faculty was prepared. Furthermore, the proposal of its establishment was discussed and definitely approved by the Scientific Council of the Institute of Chemical Technology.
On 1st April 1993 the activity of the Transport Faculty, which was given the name of Jan Perner, a 19th century railway engineer, officially began. Later that year, the first graduation ceremony of the faculty alumni was held.
The Jan Perner Transport Faculty represents continuity of the tradition established by the Railway Technical University in Prague and previously by the Czech Technical University in Prague. Thus, it follows up tradition started in 1707 by establishment of the first public engineering university in the Central Europe called Professional Engineering University in Prague. The roots of technical education, however, date back to as early as 1344, the era of an emperor Charles IV, and they are connected with a man named Mathias of Arras.