Fares have gone up by an average of 3.1 per cent, adding more than £100 to the cost of train travel for some annual season ticket holders.
Passengers across the North have endured widespread service delays and cancellations since the botched introduction of new timetables in May.
Northern services have also been disrupted by repeated strike action in a dispute over the role of guards on trains that has now entered its third calendar year.
The new fares mean the cost of an annual Leeds-Skipton season ticket has gone up by £60 to £1,960.
The price of an annual ticket for journeys between Halifax and Manchester has risen by £84 to £2,756.
Season ticket increases in other parts of the country include £148 for Brighton to London (£4,696 to £4,844), £130 for Gloucester to Birmingham (£4,108 to £4,238) and £100 for Manchester to Liverpool (£3,152 to £3,252).
Rail union leaders, politicians and campaigners are today due to stage protests against the fare rises at Leeds’s main train station and in other cities nationwide.
Leeds City Council leader Coun Judith Blake, who also leads on transport for the West Yorkshire Combined Authority, said: “The New Year should be a moment of optimism but rail passengers in the North will struggle to see the positive side as they are asked to pay higher prices today.
“Punctuality and reliability remain well below the levels required to deliver the service passengers need and our economic ambitions require.”
Henri Murison, director of the Northern Powerhouse Partnership, said commuters affected by last year’s disruption should get back the fare increases as a discount.
Criticism also came from Anthony Smith, chief executive of the Transport Focus watchdog organisation, who said: “Rail fares are going up after a year blighted by timetable chaos, poor performance and strikes.
“Until day-to-day reliability returns, with fewer significant delays and cancellations, passenger trust won’t begin to recover.”
Bruce Williamson, from campaign group Railfuture, said: “After a terrible year of timetable chaos, passengers are being rewarded with yet another kick in the wallet.”
Today’s fare rises vary slightly between different train operating companies, with Northern’s average increase coming in at 3.2 per cent.
The figure for London North Eastern Railway (LNER) – the publicly-owned operator which runs services along the flagship London-Leeds-Scotland East Coast Main Line – is 3.4 per cent.
Labour is calling on the Government to freeze prices on routes that bore the brunt of 2018’s timetable shambles.
Shadow Transport Secretary and Middlesbrough MP Andy McDonald, who is due to visit Leeds City Station today, said: “The rail fare increases are an affront to everyone who has had to endure years of chaos on Britain’s railways.”
The rises were announced at the end of November by the Rail Delivery Group, which represents private train operators and Government-owned Network Rail.
Its chief executive, Paul Plummer, said at the time: “Money from fares is underpinning the improvements to the railway that passengers want and which ultimately help boost the wider economy.”
The Department for Transport, meanwhile, acknowledged that “any fare increase is unwelcome”, but also insisted it was “not fair to ask people who do not use trains to pay more for those who do”.
Transport Secretary Chris Grayling today announced that a railcard extending half-price child fares to 16 and 17-year-olds will be introduced in time for the start of the new academic year in September.
Another new railcard aimed at 26 to 30-year-olds goes on general sale at midday today, with the Department for Transport saying it will allow an extra three million people to get a third off the cost of their travel.
Mr Grayling claimed the Government’s “record investment” in the rail network would help deliver “frequent, affordable and reliable journeys” for passengers.
He added: “Today’s announcement of a new 16 & 17 Railcard could cut the cost of travel by hundreds of pounds a year for young people and their parents.”