Passengers will pay on average 3.1% more for train tickets from 2 January, despite a disastrous year for the sector.
The rise, announced by industry body the Rail Delivery Group, could cost passengers hundreds of pounds more in annual travel costs.
Transport Focus, the passenger watchdog, greeted the news with disbelief after the chaos unleashed by the timetable changes in the summer and an autumn that has seen further disruption.
Anthony Smith, chief executive of Transport Focus, said: 'Many passengers, still reeling from summer timetable chaos and frustrated by "autumn" disruption, won’t believe fares are going up again! Until day-to-day reliability returns – with fewer significant delays and cancellations – passenger trust won’t begin to recover.
'Passengers now pour over £10bn a year into the rail industry alongside significant government investment, so the rail industry cannot be short of funding. When will this translate into a more reliable railway and better value for money for passengers?
'It’s also time for a fairer, clearer fares formula based on a calculation that uses the Consumer Prices Index, rather than the discredited Retail Price Index.'
Regulated fares, which cover about 45% of fares on national rail and include season tickets, are set to rise by 3.2% this year - the level of RPI inflation announced in July.
Train operating companies decide themselves how much to increase the rest – including advance and peak long-distance tickets.
Paul Plummer, chief executive of the Rail Delivery Group, which brings together train companies and Network Rail, said: 'Nobody wants to pay more to travel, especially those who experienced significant disruption earlier this year.
'Money from fares is underpinning the improvements to the railway that passengers want and which ultimately help boost the wider economy. That means more seats, extra services and better connections right across the country.'
In a statement, the Rail Delivery Group added this is the fourth time in the last six years that fares have been held below the previous July’s RPI inflation rate.
'98p from every £1 spent on fares goes into running the railway with fares covering day-today costs and government investment effectively funding infrastructure improvements,' the group said.
Andy McDonald MP, Labour’s shadow transport secretary, said: 'With fuel duty frozen over the last 8 years while bus and rail fares have been allowed to soar, it’s difficult not to conclude that this Government is anti-public transport.
'Chris Grayling has presided over a disastrous loss of public faith in the railway. The Government should have limited the fare rise to the Consumer Price Index to prevent fares rising in real terms and made responsible train companies freeze fares on routes affected by the timetabling chaos.'