FGW said the price changes were designed to manage capacity
Many passengers using First Great Western (FGW) will see their fares rise by up to 20%.
From 6 September FGW will introduce new restrictions on its cheapest off-peak return tickets for people travelling between the west of England and London.
This means some customers will either have to travel later in the day or pay more for their journey. Off-peak single ticket prices will be reduced.
The price rises have been criticised by groups representing passengers.
FGW spokesman Dan Panes said the price rises were needed to achieve a more even spread of passengers throughout the day.
"One of our challenges is to balance the need to encourage more customers to use our services while generating more income and managing capacity on our busy trains," he said.
Chris Irwin, the chairman of TravelWatch SouthWest, said: "We welcome the cut in the price of off-peak single tickets. But we deplore FirstGroup's decision to restrict the availability of the cheapest turn-up-and-go return tickets.
"Hard-pressed passengers will be priced off the trains. This is legalised mugging: the government must change its rules."
Under the changes which are due to come into effect in September, passengers travelling from Bristol to London who currently use the 0900 BST train at a return cost of £49 will have to pay £59.
Ashwin Kumar, Passenger Focus director, said: "Passengers who have to travel at these times will find it hard to believe they are being asked to pay such increases when inflation is so low.
"This comes on top of First Great Western increasing their car-parking charges by 25%."