The Rail Authority was established by Act No. 266/1994 Coll., the Act to Regulate Railways and Other Guided Transport Systems (hereinafter referred to as “the Railways Act”) on 1 January 1995. From the outset, the Authority was envisaged as an administrative authority that would perform state administration in the field of railways and other guided transport systems. Its headquarters were set up in Prague (the headquarters are located in the northern part of the historic Fanta building of the Prague main railway station). In addition, regional branches were established in Prague, Brno, Ostrava, Plzeň, Olomouc, Ústí nad Labem, Hradec Králové, Breclav, Žatec and Letohrad. At present, there are only three regional departments - in Prague, Plzeň and Olomouc. The number of employees has gradually decreased due to reorganisations (for example, in 2004, 134 staff members worked at the Authority; currently, there are 113 people working in various positions).
Since its foundation, the Rail Authority has been dealing with railways, tramways, trolleybuses, cableways and special (metro) rail systems.
Since 2015, when the Civil Service Act came into force, the Rail Authority has become one of the many state institutions bearing the designation of a service authority.Since its creation, the Authority has been headed by several directors. The first director of the Rail Authority was Jaroslav Vrána, who was succeeded by Tomáš Stone. After his removal, the management of the Authority was temporarily entrusted to Miroslav Dvořák. The longest serving director of the Rail Authority was Pavel Kodym, who held the position for ten years. In 2013, he was replaced by Jiří Hanuš, following a decision of the then Minister of Transport Zdeněk Žák. Jiří Hanuš managed the Authority for 10 months. He was subsequently replaced by Jiří Kolář, who was appointed to the position of director in his place and who also won the selection procedure on 1 April 2016 and again within the framework of the revision of the Civil Service Act in 2023. On 1 August 2023, he was appointed to the position by State Secretary Mgr. Martin Vavřina.