It marks the largest fares hike for passengers since 2013, when fares increased by 3.9%.
The average price for a ticket is set to go up by 3.4% on January 2, according to industry body the Rail Delivery Group.
Unions said it was "another kick in the teeth" for passengers paying the highest fares in Europe.
A spokeswoman said the firm is investing in new and improved trains, better stations and more services to "transform local rail" by 2020, and "fares are an important factor" in achieving this.
Passenger watchdog Transport Focus compared the news to "a chill wind" for customers.
More than 97p in every pound from fares goes back into improving and running the railway, the RDG said, highlighting that private investment in rail reached a record £925m in 2016-17.
One in nine trains (12%) failed to meet its punctuality target in the past year - meaning they arrived more than five minutes late for commuter services or 10 minutes late for long-distance journeys.
That means they arrived at terminating stations more than five minutes late for commuter services or 10 minutes late for long-distance journeys.
Paul Plummer, chief executive of the Rail Delivery Group which brings together train companies and Network Rail, said: "Government controls increases to nearly half of fares, including season tickets, with the rest heavily influenced by the payments train companies make to government".
It said fewer than half (47%) of passengers are satisfied with the value for money of train tickets.
The RDG said private sector investment would help deliver improvements, including 5,700 new train carriages by 2021.
The increase affects both regulated fares, which includes season tickets, and unregulated fares, such as off-peak leisure tickets.
Manuel Cortes, general secretary of the Transport Salaried Staffs Association, warned that rail users were being "bled dry to ensure our private train companies stay in profit".
The rise in regulated fares had already been capped at July's Retail Prices Index inflation rate of 3.6%.
Average prices for operators in Scotland include Virgin Trains East Coast which is set to increase by 3.4 per cent, and Virgin Trains West Coast which is set for 3.3 per cent increase.
It has been the policy of successive governments to reduce the funding of the railways by taxpayers and increase the relative contribution of passengers.
They will be outside the Citadel on January 2 when the latest annual increase in Britain's rail fares comes into effect.
Tim Calow, chairman of the Aire Valley Rail Users' Group, said it was "difficult times" on the tracks where there were cost pressures on the railways but also on passengers' money.
"Delayed, cancelled and overcrowded trains are what springs to mind when many commuters think of their rail journey, so to ask them to pay a significantly increased fare for a poor service is wrong".