More than 28,000 prosecutions for alleged fare evasions have been declared null and void.
Northern Rail brought 28,631 prosecutions against passengers using the single justice procedure (SJP) between August 6 2020 and May 21 2024, despite not being permitted to do so.
TransPennine Express brought 41 prosecutions in January 2024.
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They were all declared null and void by Chief Magistrate Paul Goldspring during a two-minute hearing at Westminster Magistrates’ Court on Thursday.
Mr Goldspring ruled in August that six “test cases” of prosecutions for alleged fare evasion brought by train companies should be declared a “nullity”, adding that others would be dealt with in the same way.
Northern welcomed Thursday’s outcome and apologised for the “errors”.
A spokesman said: “Customers affected by the issues raised in court will be contacted directly by HM Courts and Tribunal Service. We are unable to respond to individual queries at this time.
“Northern remains committed to ensuring that all our customers are treated fairly, which means ensuring all passengers who board our trains have a valid ticket.”
The SJP was set up in 2015 to allow magistrates to decide on minor offences, such as using a television without a licence or driving without car insurance, without defendants going to court.
Rail companies were permitted to use the SJP in 2016 to privately prosecute fare evaders, but many have been brought under the Regulation of Railways Act 1889, which is not allowed under the procedure.
Further hearings will take place regarding thousands of other train fare prosecutions.
Affected cases were also prosecuted by Avanti West Coast, Greater Anglia, Great Western Railway, Arriva Rail Northern, Merseyrail and C2C, the Courts and Tribunals Service said.
The department said those affected by the ruling were prosecuted after 2018, with the “vast majority” of cases prosecuted from 2020, under either section 5(1) or section 5(3) of the Regulation of Railways Act 1889.
Those affected should wait to be contacted directly by the Courts and Tribunals Service about their case, including if they have paid a financial penalty.
