Rail passengers will have to pay more to travel from 1 January 2006.
Regulated fares which include season and Saver tickets, will rise by 3.9% – even though the retail price index was 2.9% in July 2005 but is now only 2.5%.
Unregulated fares, including cheap day returns and some advance tickets, will go up by an average of 4.5%.
The Association of Train Operating Companies said the fare increase were need to fund “big improvements”.
“Operators will continue to introduce new trains, better passenger facilities and improved travel information,” said George Muir, director general of ATOC.
ATOC said the unregulated fares were decided by “market conditions”.
On the East Coast main line unregulated fares will rise by 8.8%, on Central Trains by 6.4% and on Midland Mainline by 6.1%.
On Merseyrail services in Liverpool and Merseyside both regulated and unregulated fares are rising by 2.9%.
The Rail Passengers Council said it was dismayed at the "inflation-busting" rises.
"Good value rail travel can be had – if you can get hold of the tickets in advance," said RPC chief executive Anthony Smith.
"Many walk-on fares are now at eye-watering levels. A £202 ticket for return travel between Manchester and London bought on the day means passengers are paying nearly £50 an hour for the privilege of taking the train."
Railfuture believes rail fares are much too high and do not take account of the environmental benefits of more people going by train.
Railfuture is also calling for a national railcard giving one-third off off-peak tickets to be introduced when the fares structure is reformed.
The two-tarriff railcard has been shown to give financial and economic benefits to rail operators, the Government and the passenger.
The House of Commons transport committee is reviewing rail fares now and has the opprotunity to recommend the introduction of a national railcard.