[citation needed] During the 1990s, there was a noticeable drop in railway traffic throughout the Czech Republic, a phenomenon that coincided with a massive expansion in road transport.

[9] Prior to the late 2000s, the organisation had historically incurred losses as a matter of routine, thus necessitating the provision of subsidies from the Czech government.

[11][4] Despite this milestone, České dráhy has continued to receive government subsidies and undergo periodic reforms with the aim of cutting costs to become a routinely profitable operating concern.

However, in November of that year, it was announced that no change would occur and that ČD Cargo would remain a state-owned entity; this was reportedly due to a decision by Andrej Babiš, the Prime Minister of the Czech Republic, to veto the proposal.

[16] Two years later, RegioJet took legal action over České dráhy's pricing policy, alleging its negative impact on its business results.

[17][18] During June 2022, the European Commission claimed that, between 2012 and 2016, České dráhy and the Austrian train operator ÖBB had colluded to prevent RegioJet from obtaining long-distance coaches from the latter.

Perhaps the most prominent is the ČD Class 680 Pendolino, a high speed tilting train, which was originally intended for operating international services between Berlin, Prague, and Vienna.

[20] A successor to the Pendolino was reportedly being sought during the early 2020s;[21] the company has also declared its ambitions to build a dedicated high speed network akin to the TGV.

[22] During the 2010s, both České dráhy and freight subsidiary ČD Cargo were operating Siemens Vectron electric locomotives; these have often been leased from other companies.

[27] In November 2022, it was announced that Czech plans to subsidise electrified rail operations had been approved by the European Commission, benefitting companies such as České dráhy.

[28] That same month, plans were revealed to modernise in excess of 2,000 coaches and other rail vehicles over the next four years at an annual cost of roughly Koruna 3.5bn (142.2 million United States dollars).